diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 0eba1ed473c9..eb561f6eb33a 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -17,7 +17,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
+    - uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
       with:
         distribution: "temurin"
         java-version: "17"
@@ -30,7 +30,7 @@ runs:
     - name: Set up Python
       uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5
       with:
-        python-version: "3.11"
+        python-version: "3.13"
 
     - name: Set up nf-test
       uses: nf-core/setup-nf-test@v1
@@ -38,14 +38,6 @@ runs:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
-    - name: Install dependencies from universe repo
-      if: contains(inputs.profile, 'singularity')
-      shell: bash
-      run: |
-        sudo add-apt-repository universe
-        sudo apt-get update
-        sudo apt-get install -y uidmap squashfs-tools
-
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
       uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 #v2
diff --git a/.github/skip_nf_test.json b/.github/skip_nf_test.json
index d09e471ca83b..f1681b7112b8 100644
--- a/.github/skip_nf_test.json
+++ b/.github/skip_nf_test.json
@@ -18,6 +18,8 @@
         "modules/nf-core/cellranger/mkvdjref",
         "modules/nf-core/cellranger/multi",
         "modules/nf-core/cellranger/vdj",
+        "modules/nf-core/cellrangerarc/mkref",
+        "modules/nf-core/cellrangerarc/count",
         "modules/nf-core/cellrangerarc/mkgtf",
         "modules/nf-core/checkqc",
         "modules/nf-core/coreograph",
@@ -31,7 +33,6 @@
         "modules/nf-core/deepvariant/rundeepvariant",
         "modules/nf-core/deepvariant/vcfstatsreport",
         "modules/nf-core/doubletdetection",
-        "modules/nf-core/ensemblvep/vep",
         "modules/nf-core/fastk/fastk",
         "modules/nf-core/fastk/histex",
         "modules/nf-core/fastk/merge",
@@ -74,6 +75,8 @@
         "modules/nf-core/spaceranger/mkref",
         "modules/nf-core/spotiflow",
         "modules/nf-core/svanalyzer/svbenchmark",
+        "modules/nf-core/svtk/rdtest2vcf",
+        "modules/nf-core/svtk/standardize",
         "modules/nf-core/universc",
         "modules/nf-core/vt/decompose",
         "modules/nf-core/wittyer",
@@ -85,8 +88,7 @@
         "subworkflows/nf-core/deepvariant",
         "subworkflows/nf-core/fasta_newick_epang_gappa",
         "subworkflows/nf-core/fastq_align_bamcmp_bwa",
-        "subworkflows/nf-core/fastq_align_bwa",
-        "subworkflows/nf-core/vcf_annotate_ensemblvep"
+        "subworkflows/nf-core/fastq_align_bwa"
     ],
     "docker": ["modules/nf-core/parabricks", "subworkflows/nf-core/deepvariant/tests/equality"],
     "singularity": [
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 53d0df3bec4d..a28be5ecba78 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -85,28 +85,24 @@ jobs:
         with:
           script: |
             return [...new Set(${{ steps.filter.outputs.modules_files }}
+              .filter(x => x.endsWith('main.nf'))
               .map(path => path
                 .replace('modules/nf-core/', '')
-                .split('/')
-                .slice(0, 2)
-                .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.md'))
-                .join('/'))
+                .replace(/\/main\.nf$/, '')
               )
-            ];
+            )];
       - name: Get subworkflow name
         uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
         id: subworkflow_names
         with:
           script: |
             return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
+              .filter(x => x.endsWith('main.nf'))
               .map(path => path
                 .replace('subworkflows/nf-core/', '')
-                .split('/')
-                .slice(0, 2)
-                .filter(x => !x.startsWith('main.nf') && x !== 'tests' && x !== 'templates' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.md'))
-                .join('/'))
+                .replace(/\/main\.nf$/, '')
               )
-            ];
+            )];
 
       - name: debug
         run: |
@@ -122,7 +118,7 @@ jobs:
       - image=ubuntu22-full-x64
     name: nf-core lint modules
     needs: nf-core-changes
-    if: ${{ (needs.nf-core-changes.outputs.modules == 'true') }}
+    if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }}
     strategy:
       fail-fast: false
       matrix:
@@ -149,7 +145,7 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
+      - uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
         with:
           distribution: "temurin"
           java-version: "17"
@@ -170,7 +166,7 @@ jobs:
       - image=ubuntu22-full-x64
     name: nf-core lint subworkflows
     needs: nf-core-changes
-    if: ${{ (needs.nf-core-changes.outputs.subworkflows == 'true') }}
+    if: ${{ needs.nf-core-changes.outputs.subworkflows_files != '[]' }}
     strategy:
       fail-fast: false
       matrix:
diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml
index 349227eb1106..fa7bd453c7f6 100644
--- a/.github/workflows/nf-test-gpu.yml
+++ b/.github/workflows/nf-test-gpu.yml
@@ -127,7 +127,7 @@ jobs:
   confirm-pass-gpu:
     runs-on:
       - runs-on=${{ github.run_id }}-confirm-pass-gpu
-      - runner=4cpu-linux-x64
+      - runner=2cpu-linux-x64
       - image=ubuntu22-full-x64
     needs: [nf-test-gpu]
     if: always()
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index 3033309643c6..2cdff6f5606a 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -100,12 +100,8 @@ jobs:
             tags: bwa/samse
           - profile: conda
             tags: cellpose
-          - profile: conda
-            tags: cellrangerarc/count
           - profile: conda
             tags: cellrangerarc/mkfastq
-          - profile: conda
-            tags: cellrangerarc/mkref
           - profile: conda
             tags: cellrangeratac/count
           - profile: conda
@@ -228,6 +224,8 @@ jobs:
             tags: subworkflows/fasta_clean_fcs
           - profile: conda
             tags: svanalyzer/svbenchmark
+          - profile: conda
+            tags: svtk/standardize
           - profile: conda
             tags: universc
           - profile: singularity
@@ -255,7 +253,7 @@ jobs:
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
 
-      - uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
+      - uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
         with:
           distribution: "temurin"
           java-version: "17"
diff --git a/.github/workflows/update-gpu-snapshot.yml b/.github/workflows/update-gpu-snapshot.yml
new file mode 100644
index 000000000000..8f8581f7d096
--- /dev/null
+++ b/.github/workflows/update-gpu-snapshot.yml
@@ -0,0 +1,99 @@
+name: update-gpu-snapshot
+run-name: update gpu snapshot (automated)
+on:
+  issue_comment:
+    types: [created]
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFT_VER: "0.9.2"
+  NXF_ANSI_LOG: false
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VER: "24.10.2"
+
+jobs:
+  update-gpu-snapshot:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot update gpu snapshot') &&
+      github.repository == 'nf-core/modules'
+    runs-on: "runs-on=${{ github.run_id }}/family=g4dn.xlarge/image=ubuntu24-gpu-x64"
+    steps:
+      # indication that the snapshot is being updated
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      - name: Get the test path from the comment (after "@nf-core-bot update gpu snapshot path:")
+        id: get-test-path
+        run: |
+          echo "test_path=$(echo ${{ github.event.comment.body }} | grep -oP 'path:\s*\K[^ ]+')" >> $GITHUB_OUTPUT
+
+      - name: if test path is empty, exit
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        if: steps.get-test-path.outputs.test_path == ''
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "-1"
+
+      - name: if test path is empty, exit
+        if: steps.get-test-path.outputs.test_path == ''
+        run: exit 0
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ env.NXF_VER }}"
+
+      - name: Set up Python
+        uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5
+        with:
+          python-version: "3.13"
+
+      - name: Set up nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: "${{ env.NFT_VER }}"
+          install-pdiff: true
+
+      - name: Update gpu snapshot
+        id: update-gpu-snapshot
+        run: |
+          nf-test test \
+          --profile=docker,gpu \
+          --verbose \
+          --ci \
+          --update-snapshot \
+          --filter process,workflow \
+          --tag gpu \
+          ${{ steps.get-test-path.outputs.test_path }}
+
+      - name: Commit & push changes
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Update gpu snapshot"
+          git push
diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index f029c3a24e45..7297b30b1e92 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -31,7 +31,7 @@ jobs:
 
       - name: Find conda differences
         id: conda-diff
-        uses: tj-actions/changed-files@823fcebdb31bb35fdf2229d9f769b400309430d0 # v46
+        uses: tj-actions/changed-files@ed68ef82c095e0d48ec87eccea555d944a631a4c # v46
         with:
           json: true
           escape_json: false
@@ -40,7 +40,7 @@ jobs:
 
       - name: Find Dockerfile differences
         id: docker-diff
-        uses: tj-actions/changed-files@823fcebdb31bb35fdf2229d9f769b400309430d0 # v46
+        uses: tj-actions/changed-files@ed68ef82c095e0d48ec87eccea555d944a631a4c # v46
         with:
           json: true
           escape_json: false
diff --git a/modules/nf-core/artic/guppyplex/environment.yml b/modules/nf-core/artic/guppyplex/environment.yml
index fd739b2cf0d6..9c016bcf2e1f 100644
--- a/modules/nf-core/artic/guppyplex/environment.yml
+++ b/modules/nf-core/artic/guppyplex/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::artic=1.2.3
+  - bioconda::artic=1.6.2
diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf
index e2c2f16ca068..8b4f819bda8a 100644
--- a/modules/nf-core/artic/guppyplex/main.nf
+++ b/modules/nf-core/artic/guppyplex/main.nf
@@ -4,8 +4,8 @@ process ARTIC_GUPPYPLEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a747cc579edfc0cb2176b749afc02550ab5de678ae6a40d2cfadeba6c0de25d/data' :
+        'community.wave.seqera.io/library/artic:1.6.2--d4956cdc155b8612' }"
 
     input:
     tuple val(meta), path(fastq_dir)
diff --git a/modules/nf-core/artic/guppyplex/tests/main.nf.test.snap b/modules/nf-core/artic/guppyplex/tests/main.nf.test.snap
index 93a3828d4ee4..da0ef8580c7c 100644
--- a/modules/nf-core/artic/guppyplex/tests/main.nf.test.snap
+++ b/modules/nf-core/artic/guppyplex/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9ac5b3d9c4223377c632a78e7e727718"
+                    "versions.yml:md5,2a341fa8dedc91b0567c7f0d2d2b06c6"
                 ],
                 "fastq": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9ac5b3d9c4223377c632a78e7e727718"
+                    "versions.yml:md5,2a341fa8dedc91b0567c7f0d2d2b06c6"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-01T21:05:25.082921858"
+        "timestamp": "2025-04-01T18:10:48.250223227"
     },
     "sarscov2 - fastq": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9ac5b3d9c4223377c632a78e7e727718"
+                    "versions.yml:md5,2a341fa8dedc91b0567c7f0d2d2b06c6"
                 ],
                 "fastq": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9ac5b3d9c4223377c632a78e7e727718"
+                    "versions.yml:md5,2a341fa8dedc91b0567c7f0d2d2b06c6"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-01T20:33:57.000960789"
+        "timestamp": "2025-04-01T18:10:05.440090167"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/artic/minion/environment.yml b/modules/nf-core/artic/minion/environment.yml
index a0a6221d7722..c4ed3fd375a0 100644
--- a/modules/nf-core/artic/minion/environment.yml
+++ b/modules/nf-core/artic/minion/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::artic=1.6.1
-  - bioconda::htslib=1.17
+  - bioconda::artic=1.6.2
+  - bioconda::htslib=1.17 # can't be updated due to dependency issues
diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf
index 2f9a7c9ccf6b..77bffb24f63d 100644
--- a/modules/nf-core/artic/minion/main.nf
+++ b/modules/nf-core/artic/minion/main.nf
@@ -4,8 +4,8 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
-        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a747cc579edfc0cb2176b749afc02550ab5de678ae6a40d2cfadeba6c0de25d/data' :
+        'community.wave.seqera.io/library/artic:1.6.2--d4956cdc155b8612' }"
 
     input:
     tuple val(meta), path(fastq)
diff --git a/modules/nf-core/artic/minion/tests/main.nf.test.snap b/modules/nf-core/artic/minion/tests/main.nf.test.snap
index eae31144b6d4..980aa7ea885a 100644
--- a/modules/nf-core/artic/minion/tests/main.nf.test.snap
+++ b/modules/nf-core/artic/minion/tests/main.nf.test.snap
@@ -57,7 +57,7 @@
                     
                 ],
                 "11": [
-                    "versions.yml:md5,f76ecd36f1daeb56daeb64400adf160b"
+                    "versions.yml:md5,a23b17af33ceec7bef2296a0bfb27d19"
                 ],
                 "2": [
                     [
@@ -258,20 +258,20 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f76ecd36f1daeb56daeb64400adf160b"
+                    "versions.yml:md5,a23b17af33ceec7bef2296a0bfb27d19"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-02T13:22:56.372935027"
+        "timestamp": "2025-04-01T18:17:05.880162679"
     },
     "sarscov2 - fastq": {
         "content": [
             [
-                "versions.yml:md5,f76ecd36f1daeb56daeb64400adf160b"
+                "versions.yml:md5,a23b17af33ceec7bef2296a0bfb27d19"
             ],
             [
                 [
@@ -372,8 +372,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-02T13:25:08.780155357"
+        "timestamp": "2025-04-01T18:16:19.688747943"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bandage/image/environment.yml b/modules/nf-core/bandage/image/environment.yml
index 7a672e39b7ac..06aba8a73ef5 100644
--- a/modules/nf-core/bandage/image/environment.yml
+++ b/modules/nf-core/bandage/image/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bandage=0.8.1
+  - bioconda::bandage=0.9.0
diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf
index f6801d0a3a61..016cb9c447d0 100644
--- a/modules/nf-core/bandage/image/main.nf
+++ b/modules/nf-core/bandage/image/main.nf
@@ -4,8 +4,8 @@ process BANDAGE_IMAGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' :
-        'biocontainers/bandage:0.8.1--hc9558a2_2' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3e/3eabbd074e3bc45e2643783450330cae3afc6697fefc635755ab964dc43665a1/data' :
+        'community.wave.seqera.io/library/bandage:0.9.0--4f0567049a14ea6d' }"
 
     input:
     tuple val(meta), path(gfa)
@@ -27,7 +27,7 @@ process BANDAGE_IMAGE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bandage: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        bandage: \$(echo \$(export QT_QPA_PLATFORM=offscreen; Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/bandage/image/tests/main.nf.test.snap b/modules/nf-core/bandage/image/tests/main.nf.test.snap
index 1f260eca921b..b25bc3443f57 100644
--- a/modules/nf-core/bandage/image/tests/main.nf.test.snap
+++ b/modules/nf-core/bandage/image/tests/main.nf.test.snap
@@ -10,13 +10,13 @@
                 "</defs>"
             ],
             [
-                "versions.yml:md5,443fd5f11eb36f013a1863e66d0eea21"
+                "versions.yml:md5,fbde52dd28ce0b0245e301c7a3fd4629"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-26T15:18:46.613049"
+        "timestamp": "2025-04-02T14:07:25.265702735"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/annotate/environment.yml
+++ b/modules/nf-core/bcftools/annotate/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf
index b6b73309b893..8ab067d80bd0 100644
--- a/modules/nf-core/bcftools/annotate/main.nf
+++ b/modules/nf-core/bcftools/annotate/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_ANNOTATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(input), path(index), path(annotations), path(annotations_index)
diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
index 16828b6ce04f..63e0d9d5a4ea 100644
--- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
@@ -23,79 +23,16 @@
                 
             ],
             [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T14:02:05.809043894"
+        "timestamp": "2025-04-01T12:55:30.265471036"
     },
-    "bcf": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_ann.bcf"
-                ]
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-12T16:39:33.331888"
-    },
-    "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz"
-                ]
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-06T14:01:32.326248064"
-    },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz"
-                ]
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-06T14:01:17.821142466"
-    },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub": {
         "content": [
             {
                 "0": [
@@ -108,31 +45,19 @@
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "2": [
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
                 ],
                 "csi": [
                     
                 ],
                 "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "vcf": [
                     [
@@ -144,62 +69,57 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T14:03:12.574479421"
+        "timestamp": "2025-04-01T12:55:48.340271359"
     },
-    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub": {
+    "bcf": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-                ],
-                "csi": [
-                    
-                ],
-                "tbi": [
-                    
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_ann.bcf"
                 ]
-            }
+            ],
+            [
+                "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
+            ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T14:02:38.89910979"
+        "timestamp": "2025-04-01T12:55:37.270860052"
+    },
+    "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz"
+                ]
+            ],
+            [
+                "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-01T12:55:12.451788461"
     },
     "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub": {
         "content": [
@@ -226,7 +146,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
                 ],
                 "csi": [
                     [
@@ -250,15 +170,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T14:02:49.803045339"
+        "timestamp": "2025-04-01T12:55:52.305248991"
     },
     "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub": {
         "content": [
@@ -285,7 +205,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
                 ],
                 "csi": [
                     [
@@ -309,15 +229,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T14:03:00.654715777"
+        "timestamp": "2025-04-01T12:55:59.210314307"
     },
     "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index": {
         "content": [
@@ -343,14 +263,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T14:01:45.446114465"
+        "timestamp": "2025-04-01T12:55:19.532491092"
     },
     "sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index": {
         "content": [
@@ -364,14 +284,35 @@
                 ]
             ],
             [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T13:58:14.280394724"
+        "timestamp": "2025-04-01T12:55:44.331095545"
+    },
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz"
+                ]
+            ],
+            [
+                "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-01T12:55:08.604415962"
     },
     "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi": {
         "content": [
@@ -397,13 +338,72 @@
                 ]
             ],
             [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+                "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-01T12:55:23.309288135"
+    },
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T14:01:55.70445216"
+        "timestamp": "2025-04-01T12:56:06.054536287"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/call/environment.yml b/modules/nf-core/bcftools/call/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/call/environment.yml
+++ b/modules/nf-core/bcftools/call/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/call/main.nf b/modules/nf-core/bcftools/call/main.nf
index bbb807aa0fe6..cb6790fae1c6 100644
--- a/modules/nf-core/bcftools/call/main.nf
+++ b/modules/nf-core/bcftools/call/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_CALL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/nf-core/bcftools/call/tests/main.nf.test.snap b/modules/nf-core/bcftools/call/tests/main.nf.test.snap
index 661f339a329c..977b1fc07d96 100644
--- a/modules/nf-core/bcftools/call/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/call/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                    "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
                 ],
                 "csi": [
                     [
@@ -48,15 +48,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                    "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T14:04:21.229055797"
+        "timestamp": "2025-04-01T13:04:24.254705466"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": {
         "content": [
@@ -82,14 +82,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T14:03:23.262696017"
+        "timestamp": "2025-04-01T13:03:59.28663659"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": {
         "content": [
@@ -116,7 +116,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                    "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
                 ],
                 "csi": [
                     [
@@ -140,15 +140,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                    "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T15:55:33.974136118"
+        "timestamp": "2025-04-01T13:04:17.359594287"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": {
         "content": [
@@ -175,7 +175,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                    "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
                 ],
                 "csi": [
                     
@@ -199,15 +199,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                    "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T14:04:31.830619665"
+        "timestamp": "2025-04-01T13:04:27.978617504"
     },
     "sarscov2 - [vcf, tbi], vcf, tsv, []": {
         "content": [
@@ -221,27 +221,27 @@
                 ]
             ],
             [
-                "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:59.554229257"
+        "timestamp": "2025-04-01T13:04:03.898844714"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
             "out.vcf.gz",
             [
-                "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:15:04.51091878"
+        "timestamp": "2025-04-01T13:04:10.669558689"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": {
         "content": [
@@ -267,14 +267,14 @@
                 
             ],
             [
-                "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T08:07:33.605528054"
+        "timestamp": "2025-04-01T13:03:48.669131563"
     },
     "sarscov2 - [vcf, tbi], [], [], []": {
         "content": [
@@ -288,14 +288,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:54.133768522"
+        "timestamp": "2025-04-01T13:03:41.236931778"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": {
         "content": [
@@ -321,13 +321,13 @@
                 
             ],
             [
-                "versions.yml:md5,b58bd6083a4bfe915e9e5df7d2f29f9a"
+                "versions.yml:md5,f334a077a9dce5b398e8ba2ac9f77c97"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T14:03:12.081958194"
+        "timestamp": "2025-04-01T13:03:55.541423348"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/concat/environment.yml
+++ b/modules/nf-core/bcftools/concat/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
index 8a0328cf633d..fc756e11d824 100644
--- a/modules/nf-core/bcftools/concat/main.nf
+++ b/modules/nf-core/bcftools/concat/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_CONCAT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbi)
diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
index 4f6cf8abaa57..fc3630e1d1ed 100644
--- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
@@ -21,14 +21,14 @@
                 
             ],
             [
-                "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                "versions.yml:md5,6640b543bdeba692970e302474aaee22"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-26T11:03:36.575719606"
+        "timestamp": "2025-04-01T13:07:59.602632725"
     },
     "homo_sapiens - [[vcf1, vcf2], []]": {
         "content": [
@@ -48,7 +48,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ],
                 "csi": [
                     
@@ -65,15 +65,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-01-27T13:59:01.079183608"
+        "timestamp": "2025-04-01T13:08:10.612937747"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
         "content": [
@@ -93,7 +93,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ],
                 "csi": [
                     
@@ -110,15 +110,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-01-27T13:53:58.83709764"
+        "timestamp": "2025-04-01T13:08:14.560167356"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": {
         "content": [
@@ -143,7 +143,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ],
                 "csi": [
                     [
@@ -165,15 +165,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-26T11:04:11.178539482"
+        "timestamp": "2025-04-01T13:08:21.582631265"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": {
         "content": [
@@ -197,14 +197,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                "versions.yml:md5,6640b543bdeba692970e302474aaee22"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-26T11:03:44.618596639"
+        "timestamp": "2025-04-01T13:08:06.771571575"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": {
         "content": [
@@ -224,7 +224,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ],
                 "csi": [
                     
@@ -241,15 +241,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-01-27T13:52:50.457367833"
+        "timestamp": "2025-04-01T13:07:47.748357665"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": {
         "content": [
@@ -273,14 +273,14 @@
                 
             ],
             [
-                "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                "versions.yml:md5,6640b543bdeba692970e302474aaee22"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-26T11:03:21.607274757"
+        "timestamp": "2025-04-01T13:07:55.303850698"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": {
         "content": [
@@ -305,7 +305,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ],
                 "csi": [
                     
@@ -327,15 +327,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-26T11:04:27.332133878"
+        "timestamp": "2025-04-01T13:08:32.675839006"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": {
         "content": [
@@ -360,7 +360,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ],
                 "csi": [
                     [
@@ -382,14 +382,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+                    "versions.yml:md5,6640b543bdeba692970e302474aaee22"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-26T11:04:19.745768656"
+        "timestamp": "2025-04-01T13:08:25.698924757"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/consensus/environment.yml b/modules/nf-core/bcftools/consensus/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/consensus/environment.yml
+++ b/modules/nf-core/bcftools/consensus/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf
index 303be28dbb0d..bcff83114da7 100644
--- a/modules/nf-core/bcftools/consensus/main.nf
+++ b/modules/nf-core/bcftools/consensus/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_CONSENSUS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(fasta), path(mask)
diff --git a/modules/nf-core/bcftools/consensus/tests/main.nf.test.snap b/modules/nf-core/bcftools/consensus/tests/main.nf.test.snap
index 1a23bd6d22e2..564303f08dd9 100644
--- a/modules/nf-core/bcftools/consensus/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/consensus/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                    "versions.yml:md5,f23de3ce430443d1a74a0da8bf1951eb"
                 ],
                 "fasta": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                    "versions.yml:md5,f23de3ce430443d1a74a0da8bf1951eb"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-12-20T15:38:55.13767915"
+        "timestamp": "2025-04-01T13:15:31.674308506"
     },
     "bcftools - test": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                    "versions.yml:md5,f23de3ce430443d1a74a0da8bf1951eb"
                 ],
                 "fasta": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                    "versions.yml:md5,f23de3ce430443d1a74a0da8bf1951eb"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-20T13:56:00.789333465"
+        "timestamp": "2025-04-01T13:15:23.26111289"
     },
     "bcftools - test - no mask": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                    "versions.yml:md5,f23de3ce430443d1a74a0da8bf1951eb"
                 ],
                 "fasta": [
                     [
@@ -88,14 +88,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b5e1ca5013c29fa37855fe929fb21a65"
+                    "versions.yml:md5,f23de3ce430443d1a74a0da8bf1951eb"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-20T13:56:07.531646148"
+        "timestamp": "2025-04-01T13:15:27.500207988"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/convert/environment.yml b/modules/nf-core/bcftools/convert/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/convert/environment.yml
+++ b/modules/nf-core/bcftools/convert/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf
index 7f4cb06da2ae..7ac883756453 100644
--- a/modules/nf-core/bcftools/convert/main.nf
+++ b/modules/nf-core/bcftools/convert/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_CONVERT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
diff --git a/modules/nf-core/bcftools/convert/tests/main.nf.test.snap b/modules/nf-core/bcftools/convert/tests/main.nf.test.snap
index 3aa96d9affc8..b8d35c32169f 100644
--- a/modules/nf-core/bcftools/convert/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/convert/tests/main.nf.test.snap
@@ -13,14 +13,14 @@
                 
             ],
             [
-                "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-22T11:50:55.026578232"
+        "timestamp": "2025-04-01T13:16:36.968705335"
     },
     "homo_sapiens - vcf1, tbi, [], fasta - to hap": {
         "content": [
@@ -49,14 +49,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-22T11:51:02.355109034"
+        "timestamp": "2025-04-01T13:16:44.372525199"
     },
     "homo_sapiens - vcf1, tbi, [], fasta - to hap - stub": {
         "content": [
@@ -104,7 +104,7 @@
                     
                 ],
                 "9": [
-                    "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                    "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
                 ],
                 "bcf": [
                     
@@ -149,15 +149,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                    "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-21T15:49:01.988438909"
+        "timestamp": "2025-04-01T13:17:00.867024505"
     },
     "homo_sapiens - vcf1, tbi, bed, fasta - to gvcf - stub": {
         "content": [
@@ -200,7 +200,7 @@
                     ]
                 ],
                 "9": [
-                    "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                    "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
                 ],
                 "bcf": [
                     
@@ -240,15 +240,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                    "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-21T14:41:45.395930996"
+        "timestamp": "2025-04-01T13:17:05.391247025"
     },
     "homo_sapiens - vcf1, tbi, [], fasta - to bcf - stub": {
         "content": [
@@ -291,7 +291,7 @@
                     
                 ],
                 "9": [
-                    "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                    "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
                 ],
                 "bcf": [
                     
@@ -331,15 +331,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                    "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-21T14:41:16.321899559"
+        "timestamp": "2025-04-01T13:16:53.506018396"
     },
     "homo_sapiens - vcf1, tbi, bed, fasta - to gvcf": {
         "content": [
@@ -355,13 +355,13 @@
                 "test3.vcf.gz.csi"
             ],
             [
-                "versions.yml:md5,b75cebea54ac69688ff5d1cbb0dda84f"
+                "versions.yml:md5,7c65c5f994949a183a87f21cdcb82a86"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-22T11:51:10.259936966"
+        "timestamp": "2025-04-01T13:16:49.158792906"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/csq/environment.yml b/modules/nf-core/bcftools/csq/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/csq/environment.yml
+++ b/modules/nf-core/bcftools/csq/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/csq/main.nf b/modules/nf-core/bcftools/csq/main.nf
index 38a348cda8a8..07216bc884b1 100644
--- a/modules/nf-core/bcftools/csq/main.nf
+++ b/modules/nf-core/bcftools/csq/main.nf
@@ -5,8 +5,8 @@ process BCFTOOLS_CSQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_1':
-        'biocontainers/bcftools:1.20--h8b25389_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
 
     input:
diff --git a/modules/nf-core/bcftools/csq/tests/main.nf.test.snap b/modules/nf-core/bcftools/csq/tests/main.nf.test.snap
index 8997e0dec824..f013b5c195e4 100644
--- a/modules/nf-core/bcftools/csq/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/csq/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "homo_sapiens": {
         "content": [
             "807319f441f639c33708781757da53ee",
-           [
-           "versions.yml:md5,13a1a38a47f60c47fd15a32552492bbf"
-           ]
+            [
+                "versions.yml:md5,020387d0de94edd20447c236d1d8843c"
+            ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-06T16:02:00.380988135"
+        "timestamp": "2025-04-01T13:19:10.581188283"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/filter/environment.yml
+++ b/modules/nf-core/bcftools/filter/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf
index 36cbf8c2be26..e7a24ae44100 100644
--- a/modules/nf-core/bcftools/filter/main.nf
+++ b/modules/nf-core/bcftools/filter/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_FILTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap
index 640907e42097..a9f51f98b09a 100644
--- a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap
@@ -17,7 +17,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ],
                 "csi": [
                     
@@ -34,15 +34,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-10-08T09:14:47.394005264"
+        "timestamp": "2025-04-01T13:22:24.959966433"
     },
     "sarscov2 - vcf_gz_index_tbi - stub": {
         "content": [
@@ -67,7 +67,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ],
                 "csi": [
                     
@@ -89,15 +89,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T13:59:08.235854993"
+        "timestamp": "2025-04-01T13:22:50.239958906"
     },
     "vcf": {
         "content": [
@@ -117,7 +117,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ],
                 "csi": [
                     
@@ -134,15 +134,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T15:20:28.427974818"
+        "timestamp": "2025-04-01T13:21:54.690638665"
     },
     "bcf output": {
         "content": [
@@ -162,7 +162,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ],
                 "csi": [
                     
@@ -179,15 +179,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T15:20:34.049236749"
+        "timestamp": "2025-04-01T13:22:20.154869487"
     },
     "sarscov2 - vcf_gz_index": {
         "content": [
@@ -211,14 +211,14 @@
                 
             ],
             [
-                "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T08:09:49.837854646"
+        "timestamp": "2025-04-01T13:22:01.831439795"
     },
     "sarscov2 - vcf_gz_index_csi": {
         "content": [
@@ -242,14 +242,14 @@
                 
             ],
             [
-                "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T13:57:19.513365022"
+        "timestamp": "2025-04-01T13:22:05.859541512"
     },
     "vcf - stub": {
         "content": [
@@ -269,7 +269,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ],
                 "csi": [
                     
@@ -286,15 +286,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T15:29:55.846566153"
+        "timestamp": "2025-04-01T13:22:32.075222142"
     },
     "sarscov2 - vcf_gz_index - stub": {
         "content": [
@@ -319,7 +319,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ],
                 "csi": [
                     [
@@ -341,15 +341,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T15:59:37.636874258"
+        "timestamp": "2025-04-01T13:22:36.252356698"
     },
     "sarscov2 - vcf_gz_index_csi - stub": {
         "content": [
@@ -374,7 +374,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ],
                 "csi": [
                     [
@@ -396,15 +396,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                    "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T13:58:46.36278584"
+        "timestamp": "2025-04-01T13:22:43.303679805"
     },
     "sarscov2 - vcf_gz_index_tbi": {
         "content": [
@@ -428,13 +428,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64"
+                "versions.yml:md5,0edcb48d30832d2ebc2895c773a4183a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T13:57:34.748836577"
+        "timestamp": "2025-04-01T13:22:13.144377611"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/index/environment.yml
+++ b/modules/nf-core/bcftools/index/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
index 408e584c8cef..66d824a1be8f 100644
--- a/modules/nf-core/bcftools/index/main.nf
+++ b/modules/nf-core/bcftools/index/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_INDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/bcftools/index/tests/main.nf.test.snap b/modules/nf-core/bcftools/index/tests/main.nf.test.snap
index b6f7b7003cce..19cdce7aadd0 100644
--- a/modules/nf-core/bcftools/index/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/index/tests/main.nf.test.snap
@@ -14,7 +14,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,b4ea0f633dba7f5992fbf41b518f98e9"
+                    "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e"
                 ],
                 "csi": [
                     [
@@ -28,15 +28,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,b4ea0f633dba7f5992fbf41b518f98e9"
+                    "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-03T11:43:09.347303629"
+        "timestamp": "2025-04-01T13:27:09.068494316"
     },
     "sarscov2 - vcf - tbi": {
         "content": [
@@ -49,14 +49,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,b4ea0f633dba7f5992fbf41b518f98e9"
+                "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-03T11:42:46.38669168"
+        "timestamp": "2025-04-01T13:27:02.067535809"
     },
     "sarscov2 - vcf - tbi - stub": {
         "content": [
@@ -73,7 +73,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b4ea0f633dba7f5992fbf41b518f98e9"
+                    "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e"
                 ],
                 "csi": [
                     
@@ -87,15 +87,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b4ea0f633dba7f5992fbf41b518f98e9"
+                    "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-03T11:43:32.494612317"
+        "timestamp": "2025-04-01T13:27:13.198252226"
     },
     "sarscov2 - vcf - csi": {
         "content": [
@@ -108,13 +108,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,b4ea0f633dba7f5992fbf41b518f98e9"
+                "versions.yml:md5,0679fa7bdb181a09497bb5d0e0208e7e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-03T11:42:33.652109509"
+        "timestamp": "2025-04-01T13:26:58.059916648"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/isec/environment.yml b/modules/nf-core/bcftools/isec/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/isec/environment.yml
+++ b/modules/nf-core/bcftools/isec/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf
index 80d18721b725..8e865a5ac377 100644
--- a/modules/nf-core/bcftools/isec/main.nf
+++ b/modules/nf-core/bcftools/isec/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_ISEC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
diff --git a/modules/nf-core/bcftools/isec/tests/main.nf.test.snap b/modules/nf-core/bcftools/isec/tests/main.nf.test.snap
index 817ca2dc9ab0..ab5e5d7ac29e 100644
--- a/modules/nf-core/bcftools/isec/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/isec/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2 - [[vcf1.gz, vcf2.gz], [tbi1, tbi2]]": {
         "content": [
             [
-                "versions.yml:md5,c5b5a1204cf56fec79d17e1913eaca27"
+                "versions.yml:md5,a3eb0a5248f50944c4df3dd78f64fcfa"
             ],
             [
                 "0000.vcf.gz",
@@ -20,10 +20,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-07-03T16:32:18.167072863"
+        "timestamp": "2025-04-01T13:34:51.49520705"
     },
     "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c5b5a1204cf56fec79d17e1913eaca27"
+                    "versions.yml:md5,a3eb0a5248f50944c4df3dd78f64fcfa"
                 ],
                 "results": [
                     [
@@ -62,14 +62,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c5b5a1204cf56fec79d17e1913eaca27"
+                    "versions.yml:md5,a3eb0a5248f50944c4df3dd78f64fcfa"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-07-03T09:45:52.881120953"
+        "timestamp": "2025-04-01T13:34:55.788476598"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/merge/environment.yml
+++ b/modules/nf-core/bcftools/merge/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
index facb14ea1316..bcca1036c5d3 100644
--- a/modules/nf-core/bcftools/merge/main.nf
+++ b/modules/nf-core/bcftools/merge/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap
index b3b62556313f..5f2ac39ec56f 100644
--- a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap
@@ -4,14 +4,14 @@
             "e0de448dc8e712956a03ce68d79a0b3a",
             "test.vcf.gz.tbi",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T12:34:16.977726522"
+        "timestamp": "2025-04-01T13:36:57.808346534"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub": {
         "content": [
@@ -28,7 +28,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -42,28 +42,28 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:17:34.532910365"
+        "timestamp": "2025-04-01T13:37:26.710546205"
     },
     "sarscov2 - [vcf, tbi], [], [], bed": {
         "content": [
             "febdcfb851dcfc83d8248520830aef10",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:29:48.630057872"
+        "timestamp": "2025-04-01T13:37:02.283952426"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub": {
         "content": [
@@ -85,7 +85,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     [
@@ -104,28 +104,28 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:17:59.983157569"
+        "timestamp": "2025-04-01T13:37:47.351607982"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf output": {
         "content": [
             "57bb84274f336465d0a0946b532093b0",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:29:05.528412678"
+        "timestamp": "2025-04-01T13:36:29.065115273"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub": {
         "content": [
@@ -142,7 +142,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -156,15 +156,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T11:58:46.619657457"
+        "timestamp": "2025-04-01T13:37:42.876870714"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub": {
         "content": [
@@ -186,7 +186,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     [
@@ -205,15 +205,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:18:12.848227353"
+        "timestamp": "2025-04-01T13:37:56.095127856"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub": {
         "content": [
@@ -230,7 +230,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -244,42 +244,42 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T11:23:15.794389239"
+        "timestamp": "2025-04-01T13:37:30.988068166"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index": {
         "content": [
             "e0de448dc8e712956a03ce68d79a0b3a",
             "test.vcf.gz.csi",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T11:57:16.850641473"
+        "timestamp": "2025-04-01T13:36:53.522123382"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output": {
         "content": [
             "e0de448dc8e712956a03ce68d79a0b3a",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T11:56:27.949031071"
+        "timestamp": "2025-04-01T13:36:33.357373822"
     },
     "sarscov2 - [vcf, tbi], [], [], bed - stub": {
         "content": [
@@ -296,7 +296,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -310,28 +310,28 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:18:19.273064822"
+        "timestamp": "2025-04-01T13:38:00.615531476"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - bcf output": {
         "content": [
             "test.bcf",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T11:56:38.567500859"
+        "timestamp": "2025-04-01T13:36:37.68065343"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub": {
         "content": [
@@ -348,7 +348,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -362,15 +362,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:17:47.356328326"
+        "timestamp": "2025-04-01T13:37:35.402926588"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - one sample - stub": {
         "content": [
@@ -387,7 +387,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -401,15 +401,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T15:13:18.708495878"
+        "timestamp": "2025-04-01T13:38:13.018206068"
     },
     "homo_sapiens - [vcf, tbi], fasta, fai, bed  - vcf.gz output - stub": {
         "content": [
@@ -426,7 +426,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -440,55 +440,55 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:56:45.706125286"
+        "timestamp": "2025-04-01T13:38:08.718741834"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index": {
         "content": [
             "e0de448dc8e712956a03ce68d79a0b3a",
             "test.vcf.gz.csi",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T12:33:43.639646108"
+        "timestamp": "2025-04-01T13:36:49.114421247"
     },
     "homo_sapiens - [vcf, tbi], fasta, fai, bed  - vcf.gz output": {
         "content": [
             "645b7f7f9131bfe350a9ec3cf82c17fe",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:55:44.299812124"
+        "timestamp": "2025-04-01T13:37:13.928323894"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - one sample": {
         "content": [
             "2a374cf02f0c32cf607646167e7f153b",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T15:37:38.491844702"
+        "timestamp": "2025-04-01T13:37:18.074920523"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
@@ -505,7 +505,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     
@@ -519,15 +519,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:17:28.188178904"
+        "timestamp": "2025-04-01T13:37:22.322283619"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub": {
         "content": [
@@ -549,7 +549,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ],
                 "index": [
                     [
@@ -568,40 +568,40 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                    "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T13:18:06.430943593"
+        "timestamp": "2025-04-01T13:37:51.791248219"
     },
     "sarscov2 - [vcf, tbi], [], [], []": {
         "content": [
             "e0de448dc8e712956a03ce68d79a0b3a",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T12:31:03.893007442"
+        "timestamp": "2025-04-01T13:36:21.537368529"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output": {
         "content": [
             "test.bcf.gz",
             [
-                "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a"
+                "versions.yml:md5,ba7e9c7697d692c11c76006d21a8411f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-05T11:56:56.416361069"
+        "timestamp": "2025-04-01T13:36:41.94604183"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/mpileup/environment.yml
+++ b/modules/nf-core/bcftools/mpileup/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
index fbac5cedb468..f712b5183e4e 100644
--- a/modules/nf-core/bcftools/mpileup/main.nf
+++ b/modules/nf-core/bcftools/mpileup/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_MPILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(bam), path(intervals)
diff --git a/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap
index a7726898826d..08c87e2f8116 100644
--- a/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/mpileup/tests/main.nf.test.snap
@@ -72,14 +72,14 @@
     "bam_fasta_false_versions": {
         "content": [
             [
-                "versions.yml:md5,6af9a67cd12c721ccc9702c17bc2f3a5"
+                "versions.yml:md5,489c9d000145be40205442e6c1be70a5"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:23.424052671"
+        "timestamp": "2025-04-01T13:44:46.083414473"
     },
     "bam_fasta_false_stub.bcftools_stats.txt": {
         "content": [
@@ -94,14 +94,14 @@
     "bam_bed_fasta_false_versions": {
         "content": [
             [
-                "versions.yml:md5,6af9a67cd12c721ccc9702c17bc2f3a5"
+                "versions.yml:md5,489c9d000145be40205442e6c1be70a5"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:44.101963218"
+        "timestamp": "2025-04-01T13:45:06.213311379"
     },
     "bam_bed_fasta_false.vcf.gz": {
         "content": [
@@ -116,14 +116,14 @@
     "bam_bed_fasta_true_versions": {
         "content": [
             [
-                "versions.yml:md5,6af9a67cd12c721ccc9702c17bc2f3a5"
+                "versions.yml:md5,489c9d000145be40205442e6c1be70a5"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:38.630394619"
+        "timestamp": "2025-04-01T13:45:01.634976363"
     },
     "bam_fasta_false.vcf.gz": {
         "content": [
@@ -208,14 +208,14 @@
     "bam_fasta_false_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,6af9a67cd12c721ccc9702c17bc2f3a5"
+                "versions.yml:md5,489c9d000145be40205442e6c1be70a5"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:28.530439931"
+        "timestamp": "2025-04-01T13:44:50.214889195"
     },
     "bam_bed_fasta_true.bcftools_stats.txt": {
         "content": [
@@ -240,14 +240,14 @@
     "bam_bed_fasta_false_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,6af9a67cd12c721ccc9702c17bc2f3a5"
+                "versions.yml:md5,489c9d000145be40205442e6c1be70a5"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:49.139377519"
+        "timestamp": "2025-04-01T13:45:10.356826049"
     },
     "bam_bed_fasta_true.mpileup.gz": {
         "content": [
@@ -262,13 +262,13 @@
     "bam_bed_fasta_true_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,6af9a67cd12c721ccc9702c17bc2f3a5"
+                "versions.yml:md5,489c9d000145be40205442e6c1be70a5"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:14:33.646218607"
+        "timestamp": "2025-04-01T13:44:57.520283217"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/norm/environment.yml
+++ b/modules/nf-core/bcftools/norm/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf
index bd7a2501278c..3b226f274840 100644
--- a/modules/nf-core/bcftools/norm/main.nf
+++ b/modules/nf-core/bcftools/norm/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_NORM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap
index 3be52116a9d9..b71721a73657 100644
--- a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap
@@ -17,7 +17,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -34,15 +34,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:38:42.639095032"
+        "timestamp": "2025-04-01T14:02:35.039667679"
     },
     "sarscov2 - [ vcf, [] ], fasta - stub": {
         "content": [
@@ -62,7 +62,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -79,15 +79,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:38:05.448449893"
+        "timestamp": "2025-04-01T14:02:19.531714933"
     },
     "sarscov2 - [ vcf, tbi ], fasta - vcf output": {
         "content": [
@@ -107,7 +107,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -124,15 +124,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:37:12.741719961"
+        "timestamp": "2025-04-01T14:01:53.57043182"
     },
     "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index - stub": {
         "content": [
@@ -157,7 +157,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     [
@@ -179,15 +179,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:39:22.875147941"
+        "timestamp": "2025-04-01T14:02:53.457953524"
     },
     "sarscov2 - [ vcf, tbi ], fasta - vcf_gz output": {
         "content": [
@@ -206,14 +206,14 @@
                 
             ],
             [
-                "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                "versions.yml:md5,cb38669b7069800497b0706a09932aec"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T08:15:23.38765384"
+        "timestamp": "2025-04-01T14:02:00.719886153"
     },
     "sarscov2 - [ vcf, [] ], fasta": {
         "content": [
@@ -233,7 +233,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -250,15 +250,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:36:21.519977754"
+        "timestamp": "2025-04-01T14:01:23.75323253"
     },
     "sarscov2 - [ vcf, tbi ], fasta - vcf output -stub": {
         "content": [
@@ -278,7 +278,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -295,15 +295,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:38:27.8230994"
+        "timestamp": "2025-04-01T14:02:30.863210572"
     },
     "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output": {
         "content": [
@@ -313,7 +313,7 @@
                         {
                             "id": "test"
                         },
-                        "test_norm.bcf:md5,f35545c26a788b5eb697d9c0490339d9"
+                        "test_norm.bcf:md5,bf88706ef69c44ca9e287bc953ba3593"
                     ]
                 ],
                 "1": [
@@ -323,7 +323,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -336,19 +336,19 @@
                         {
                             "id": "test"
                         },
-                        "test_norm.bcf:md5,f35545c26a788b5eb697d9c0490339d9"
+                        "test_norm.bcf:md5,bf88706ef69c44ca9e287bc953ba3593"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:37:53.942403192"
+        "timestamp": "2025-04-01T14:02:12.325415263"
     },
     "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi - stub": {
         "content": [
@@ -373,7 +373,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     [
@@ -395,15 +395,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T13:56:05.3799488"
+        "timestamp": "2025-04-01T14:03:00.652023677"
     },
     "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi": {
         "content": [
@@ -443,7 +443,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -460,15 +460,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:36:58.39445154"
+        "timestamp": "2025-04-01T14:01:46.207313323"
     },
     "sarscov2 - [ vcf, tbi ], fasta -stub": {
         "content": [
@@ -488,7 +488,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -505,15 +505,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:38:16.259516142"
+        "timestamp": "2025-04-01T14:02:26.686137644"
     },
     "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output - stub": {
         "content": [
@@ -533,7 +533,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -550,15 +550,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:39:10.503208929"
+        "timestamp": "2025-04-01T14:02:46.406125297"
     },
     "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index": {
         "content": [
@@ -603,7 +603,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -620,15 +620,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:38:59.121377258"
+        "timestamp": "2025-04-01T14:02:39.213092385"
     },
     "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub": {
         "content": [
@@ -653,7 +653,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -675,15 +675,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T13:56:16.404380471"
+        "timestamp": "2025-04-01T14:03:07.888046412"
     },
     "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi": {
         "content": [
@@ -728,7 +728,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ],
                 "csi": [
                     
@@ -745,14 +745,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ff760495922469e56d0fc3372773000d"
+                    "versions.yml:md5,cb38669b7069800497b0706a09932aec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:37:42.141945244"
+        "timestamp": "2025-04-01T14:02:04.993236789"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginimputeinfo/environment.yml b/modules/nf-core/bcftools/pluginimputeinfo/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/pluginimputeinfo/environment.yml
+++ b/modules/nf-core/bcftools/pluginimputeinfo/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/pluginimputeinfo/main.nf b/modules/nf-core/bcftools/pluginimputeinfo/main.nf
index b5dd93e60e25..70f4b7496c8c 100644
--- a/modules/nf-core/bcftools/pluginimputeinfo/main.nf
+++ b/modules/nf-core/bcftools/pluginimputeinfo/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINIMPUTEINFO {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_1':
-        'biocontainers/bcftools:1.20--h8b25389_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap
index 8e3b4e953891..f80b9cb95cac 100644
--- a/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                    "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
                 ],
                 "csi": [
                     [
@@ -48,15 +48,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                    "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:42:24.860002123"
+        "timestamp": "2025-04-01T14:05:04.190234681"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": {
         "content": [
@@ -82,14 +82,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:41:28.801236995"
+        "timestamp": "2025-04-01T14:04:36.397866108"
     },
     "sarscov2 - [vcf, tbi], [], []": {
         "content": [
@@ -103,14 +103,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:25:19.761202429"
+        "timestamp": "2025-04-01T14:03:15.741219914"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": {
         "content": [
@@ -137,7 +137,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                    "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
                 ],
                 "csi": [
                     [
@@ -161,15 +161,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                    "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:42:05.180443538"
+        "timestamp": "2025-04-01T14:04:56.580036692"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": {
         "content": [
@@ -196,7 +196,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                    "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
                 ],
                 "csi": [
                     
@@ -220,15 +220,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                    "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:42:49.144650301"
+        "timestamp": "2025-04-01T14:05:08.923241281"
     },
     "sarscov2 - [vcf, tbi], vcf, tsv, []": {
         "content": [
@@ -242,27 +242,27 @@
                 ]
             ],
             [
-                "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:41:40.973896543"
+        "timestamp": "2025-04-01T14:04:44.100934271"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
             "out_vcf.vcf",
             [
-                "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:41:53.257327022"
+        "timestamp": "2025-04-01T14:04:51.836211102"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": {
         "content": [
@@ -288,14 +288,14 @@
                 
             ],
             [
-                "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:41:05.386430406"
+        "timestamp": "2025-04-01T14:03:23.697136729"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": {
         "content": [
@@ -321,13 +321,13 @@
                 
             ],
             [
-                "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7"
+                "versions.yml:md5,3ee8831d520a04064c87941bc5a46b2f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-10T21:41:17.063459898"
+        "timestamp": "2025-04-01T14:04:28.601609527"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/pluginscatter/environment.yml
+++ b/modules/nf-core/bcftools/pluginscatter/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/pluginscatter/main.nf b/modules/nf-core/bcftools/pluginscatter/main.nf
index b3b6691d8ecf..95a07b1a677f 100644
--- a/modules/nf-core/bcftools/pluginscatter/main.nf
+++ b/modules/nf-core/bcftools/pluginscatter/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINSCATTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap
index 3168f91be58f..4b33f7c922b7 100644
--- a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap
@@ -21,7 +21,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     
@@ -42,15 +42,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T15:09:19.199443051"
+        "timestamp": "2025-04-01T14:05:55.658059628"
     },
     "homo_sapiens - sites per chunk": {
         "content": [
@@ -79,7 +79,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     
@@ -105,15 +105,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:39:46.012676995"
+        "timestamp": "2025-04-01T14:05:13.744915526"
     },
     "homo_sapiens - sites per chunk - vcf_gz_index_csi - stub": {
         "content": [
@@ -146,7 +146,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     [
@@ -176,15 +176,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T15:10:12.470969127"
+        "timestamp": "2025-04-01T14:06:11.27976016"
     },
     "homo_sapiens - scatter file": {
         "content": [
@@ -207,7 +207,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     
@@ -227,15 +227,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:40:25.33705743"
+        "timestamp": "2025-04-01T14:05:44.276242643"
     },
     "homo_sapiens - scatter file - stub": {
         "content": [
@@ -259,7 +259,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     
@@ -280,15 +280,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T15:09:41.478631999"
+        "timestamp": "2025-04-01T14:06:02.926688297"
     },
     "homo_sapiens - sites per chunk - vcf_gz_index - stub": {
         "content": [
@@ -321,7 +321,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     [
@@ -351,15 +351,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T15:09:59.976006697"
+        "timestamp": "2025-04-01T14:06:06.99784338"
     },
     "vcf_gz_index_tbi": {
         "content": [
@@ -382,14 +382,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-06T10:27:48.127273006"
+        "timestamp": "2025-04-01T14:05:29.650945585"
     },
     "homo_sapiens - sites per chunk - vcf_gz_index_tbi - stub": {
         "content": [
@@ -422,7 +422,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     
@@ -452,15 +452,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T15:10:37.027506409"
+        "timestamp": "2025-04-01T14:06:18.223399542"
     },
     "vcf_gz_index": {
         "content": [
@@ -483,14 +483,14 @@
                 
             ],
             [
-                "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-06T10:24:46.201810185"
+        "timestamp": "2025-04-01T14:05:21.026776365"
     },
     "vcf_gz_index_csi": {
         "content": [
@@ -513,14 +513,14 @@
                 
             ],
             [
-                "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-06T10:27:20.636624541"
+        "timestamp": "2025-04-01T14:05:25.336641966"
     },
     "homo_sapiens - scatter": {
         "content": [
@@ -540,7 +540,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     
@@ -557,15 +557,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T14:40:12.621284696"
+        "timestamp": "2025-04-01T14:05:37.031808453"
     },
     "homo_sapiens - sites per chunk - stub": {
         "content": [
@@ -589,7 +589,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ],
                 "csi": [
                     
@@ -610,14 +610,14 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf"
+                    "versions.yml:md5,2a9760179472323d4a0aff1de24f6454"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T15:08:56.987822348"
+        "timestamp": "2025-04-01T14:05:48.465950294"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginsplit/environment.yml b/modules/nf-core/bcftools/pluginsplit/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/pluginsplit/environment.yml
+++ b/modules/nf-core/bcftools/pluginsplit/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index e541df114edd..95ec5de8d7a7 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINSPLIT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf, stageAs: "input/*"), path(tbi, stageAs: "input/*")
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
index b915b7cf24ff..5ae11646ddfd 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -21,7 +21,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ],
                 "csi": [
                     
@@ -42,15 +42,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-20T14:56:54.383979416"
+        "timestamp": "2025-04-01T14:07:55.106801187"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi": {
         "content": [
@@ -112,7 +112,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ],
                 "csi": [
                     
@@ -142,15 +142,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-20T14:57:11.163588435"
+        "timestamp": "2025-04-01T14:08:06.953248081"
     },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], []": {
         "content": [
@@ -174,7 +174,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ],
                 "csi": [
                     
@@ -195,15 +195,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-20T14:56:27.978161766"
+        "timestamp": "2025-04-01T14:07:33.810970536"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub": {
         "content": [
@@ -227,7 +227,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ],
                 "csi": [
                     
@@ -248,14 +248,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                    "versions.yml:md5,b423d3a22a27c76c3b661ba6f02f42b2"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-20T14:57:02.456908152"
+        "timestamp": "2025-04-01T14:08:02.530972889"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/plugintag2tag/environment.yml b/modules/nf-core/bcftools/plugintag2tag/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/plugintag2tag/environment.yml
+++ b/modules/nf-core/bcftools/plugintag2tag/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/plugintag2tag/main.nf b/modules/nf-core/bcftools/plugintag2tag/main.nf
index b326c7dc487c..5001661eea92 100644
--- a/modules/nf-core/bcftools/plugintag2tag/main.nf
+++ b/modules/nf-core/bcftools/plugintag2tag/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINTAG2TAG {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test.snap b/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test.snap
index 651601fb2b0d..1f63d100a52d 100644
--- a/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/plugintag2tag/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                    "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
                 ],
                 "csi": [
                     [
@@ -48,15 +48,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                    "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:44:33.996543"
+        "timestamp": "2025-04-01T14:08:55.259282821"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": {
         "content": [
@@ -82,14 +82,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:42:43.348779"
+        "timestamp": "2025-04-01T14:08:32.604644796"
     },
     "sarscov2 - [vcf, tbi], [], []": {
         "content": [
@@ -103,14 +103,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T13:48:35.163391"
+        "timestamp": "2025-04-01T14:08:10.969839053"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": {
         "content": [
@@ -137,7 +137,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                    "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
                 ],
                 "csi": [
                     [
@@ -161,28 +161,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                    "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:44:06.056403"
-    },
-    "sarscov2 - [vcf, tbi], [], [] - stub": {
-        "content": [
-            "out.vcf",
-            [
-                "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-28T13:45:59.170948"
+        "timestamp": "2025-04-01T14:08:51.144054002"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": {
         "content": [
@@ -209,7 +196,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                    "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
                 ],
                 "csi": [
                     
@@ -233,15 +220,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                    "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:45:00.60121"
+        "timestamp": "2025-04-01T14:09:02.368894385"
     },
     "sarscov2 - [vcf, tbi], vcf, tsv, []": {
         "content": [
@@ -255,27 +242,27 @@
                 ]
             ],
             [
-                "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:43:10.164895"
+        "timestamp": "2025-04-01T14:08:39.853150291"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
             "out.vcf",
             [
-                "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:43:37.881451"
+        "timestamp": "2025-04-01T14:08:43.90765949"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": {
         "content": [
@@ -301,14 +288,14 @@
                 
             ],
             [
-                "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:41:46.905606"
+        "timestamp": "2025-04-01T14:08:18.282237234"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": {
         "content": [
@@ -334,13 +321,13 @@
                 
             ],
             [
-                "versions.yml:md5,0206fd0262717f5283f961e147fb9759"
+                "versions.yml:md5,9ff5c94e03f6e826ee6e880d3b7456f5"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-28T15:42:15.499991"
+        "timestamp": "2025-04-01T14:08:25.610882259"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/query/environment.yml
+++ b/modules/nf-core/bcftools/query/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
index 58019f4d8668..52be34b1a505 100644
--- a/modules/nf-core/bcftools/query/main.nf
+++ b/modules/nf-core/bcftools/query/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_QUERY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap
index 3ead1f2c5c05..beee2ef24c58 100644
--- a/modules/nf-core/bcftools/query/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/query/tests/main.nf.test.snap
@@ -10,27 +10,27 @@
                 ]
             ],
             [
-                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+                "versions.yml:md5,e0542833ae6a03a85611e22dbf0921b6"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:15:44.916249758"
+        "timestamp": "2025-04-01T14:09:16.570707353"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
             "out.txt",
             [
-                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+                "versions.yml:md5,e0542833ae6a03a85611e22dbf0921b6"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:15:49.932359271"
+        "timestamp": "2025-04-01T14:09:23.462432361"
     },
     "sarscov2 - [vcf, tbi], [], [], []": {
         "content": [
@@ -43,13 +43,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+                "versions.yml:md5,e0542833ae6a03a85611e22dbf0921b6"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:15:39.930697926"
+        "timestamp": "2025-04-01T14:09:09.337957177"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/reheader/environment.yml
+++ b/modules/nf-core/bcftools/reheader/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf
index 9cf6d0d38be1..37062ab141a5 100644
--- a/modules/nf-core/bcftools/reheader/main.nf
+++ b/modules/nf-core/bcftools/reheader/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_REHEADER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(header), path(samples)
diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap
index 87a3654a5477..fc8dfd58b189 100644
--- a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap
@@ -20,14 +20,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T10:09:05.955833763"
+        "timestamp": "2025-04-01T14:09:50.163995386"
     },
     "sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub": {
         "content": [
@@ -51,7 +51,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     [
@@ -72,15 +72,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:52:41.444952182"
+        "timestamp": "2025-04-01T14:10:22.786980419"
     },
     "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub": {
         "content": [
@@ -104,7 +104,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     [
@@ -125,15 +125,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:53:04.314827944"
+        "timestamp": "2025-04-01T14:10:30.908145496"
     },
     "sarscov2 - [vcf, [], []], fai - vcf output": {
         "content": [
@@ -151,7 +151,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     
@@ -166,15 +166,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:50:41.983008108"
+        "timestamp": "2025-04-01T14:09:27.878225575"
     },
     "sarscov2 - [vcf, [], []], fai - bcf output": {
         "content": [
@@ -192,7 +192,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     
@@ -207,15 +207,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:51:43.072513252"
+        "timestamp": "2025-04-01T14:09:57.340213283"
     },
     "sarscov2 - [vcf, [], []], fai - vcf.gz output": {
         "content": [
@@ -233,7 +233,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     
@@ -248,15 +248,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:50:53.055630152"
+        "timestamp": "2025-04-01T14:09:32.00582809"
     },
     "sarscov2 - [vcf, [], []], fai - vcf.gz output - index": {
         "content": [
@@ -279,14 +279,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T10:08:37.999924355"
+        "timestamp": "2025-04-01T14:09:38.993337881"
     },
     "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub": {
         "content": [
@@ -310,7 +310,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     [
@@ -331,28 +331,28 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:52:52.512269206"
+        "timestamp": "2025-04-01T14:10:26.882028182"
     },
     "sarscov2 - [vcf, [], []], fai - stub": {
         "content": [
             "tested.vcf",
             [
-                "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:16:36.337112514"
+        "timestamp": "2025-04-01T14:10:15.695515447"
     },
     "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index": {
         "content": [
@@ -375,14 +375,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T10:08:55.434831174"
+        "timestamp": "2025-04-01T14:09:43.054413402"
     },
     "sarscov2 - [vcf, [], samples], fai": {
         "content": [
@@ -400,7 +400,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     
@@ -415,15 +415,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:52:12.216002665"
+        "timestamp": "2025-04-01T14:10:11.620196263"
     },
     "sarscov2 - [vcf, header, []], []": {
         "content": [
@@ -441,7 +441,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ],
                 "index": [
                     
@@ -456,14 +456,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                    "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-09-03T09:51:54.062386022"
+        "timestamp": "2025-04-01T14:10:04.588597619"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/roh/environment.yml b/modules/nf-core/bcftools/roh/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/roh/environment.yml
+++ b/modules/nf-core/bcftools/roh/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf
index ac96eef54f34..a884600371c5 100644
--- a/modules/nf-core/bcftools/roh/main.nf
+++ b/modules/nf-core/bcftools/roh/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_ROH {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test.snap b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap
index 3b008a01e989..d2d0fbd14845 100644
--- a/modules/nf-core/bcftools/roh/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap
@@ -7,30 +7,30 @@
                         {
                             "id": "test"
                         },
-                        "test.roh:md5,853de778be3030754be40e11be0aa557"
+                        "test.roh:md5,c6151714701971c414f43242028d6644"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+                    "versions.yml:md5,bebe8b809113814bd900c719e63ca541"
                 ],
                 "roh": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.roh:md5,853de778be3030754be40e11be0aa557"
+                        "test.roh:md5,c6151714701971c414f43242028d6644"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+                    "versions.yml:md5,bebe8b809113814bd900c719e63ca541"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-26T14:19:06.961553"
+        "timestamp": "2025-04-01T14:10:35.126856008"
     },
     "test-bcftools-roh-stub": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+                    "versions.yml:md5,bebe8b809113814bd900c719e63ca541"
                 ],
                 "roh": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+                    "versions.yml:md5,bebe8b809113814bd900c719e63ca541"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-26T14:19:11.161719"
+        "timestamp": "2025-04-01T14:10:42.12971505"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/sort/environment.yml
+++ b/modules/nf-core/bcftools/sort/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf
index 7d4c9b8e9df3..6cbd09b593a7 100644
--- a/modules/nf-core/bcftools/sort/main.nf
+++ b/modules/nf-core/bcftools/sort/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_SORT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap
index f38272cb2874..f092dbf591fa 100644
--- a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap
@@ -22,7 +22,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ],
                 "csi": [
                     
@@ -44,15 +44,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:06:05.201680777"
+        "timestamp": "2025-04-01T14:11:26.694501734"
     },
     "vcf": {
         "content": [
@@ -72,7 +72,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ],
                 "csi": [
                     
@@ -89,15 +89,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:04:43.889971134"
+        "timestamp": "2025-04-01T14:10:49.218451505"
     },
     "sarscov2 - vcf_gz_index": {
         "content": [
@@ -121,14 +121,14 @@
                 
             ],
             [
-                "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                "versions.yml:md5,54b077078de3c204fb81688af4aae489"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:04:55.385964497"
+        "timestamp": "2025-04-01T14:10:56.259159613"
     },
     "sarscov2 - vcf_gz_index_csi": {
         "content": [
@@ -152,14 +152,14 @@
                 
             ],
             [
-                "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                "versions.yml:md5,54b077078de3c204fb81688af4aae489"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:05:06.662818922"
+        "timestamp": "2025-04-01T14:11:00.358141543"
     },
     "sarscov2 - vcf_gz_index - stub": {
         "content": [
@@ -184,7 +184,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ],
                 "csi": [
                     [
@@ -206,15 +206,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:05:40.012912381"
+        "timestamp": "2025-04-01T14:11:18.590986384"
     },
     "sarscov2 - vcf_gz_index_csi - stub": {
         "content": [
@@ -239,7 +239,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ],
                 "csi": [
                     [
@@ -261,15 +261,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:05:52.405673587"
+        "timestamp": "2025-04-01T14:11:22.65765844"
     },
     "sarscov2 - vcf - stub": {
         "content": [
@@ -289,7 +289,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ],
                 "csi": [
                     
@@ -306,15 +306,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                    "versions.yml:md5,54b077078de3c204fb81688af4aae489"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:05:29.117946461"
+        "timestamp": "2025-04-01T14:11:11.501401617"
     },
     "sarscov2 - vcf_gz_index_tbi": {
         "content": [
@@ -338,13 +338,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb"
+                "versions.yml:md5,54b077078de3c204fb81688af4aae489"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:05:17.217274984"
+        "timestamp": "2025-04-01T14:11:07.401740499"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/split/environment.yml b/modules/nf-core/bcftools/split/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/split/environment.yml
+++ b/modules/nf-core/bcftools/split/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/split/main.nf b/modules/nf-core/bcftools/split/main.nf
index 72a582f32f9c..5d61a3bbd939 100644
--- a/modules/nf-core/bcftools/split/main.nf
+++ b/modules/nf-core/bcftools/split/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_SPLIT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test.snap b/modules/nf-core/bcftools/split/tests/main.nf.test.snap
index c1a3c98578c1..1b8f8e95ae37 100644
--- a/modules/nf-core/bcftools/split/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/split/tests/main.nf.test.snap
@@ -3,13 +3,13 @@
         "content": [
             "ecf3973f634b7baa1c13e60bfb77a174",
             [
-                "versions.yml:md5,a1c58d82f1e5c0fed394bfb865f57fd9"
+                "versions.yml:md5,046174c10cfa782e8acf3bdc9528729f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-26T14:16:45.077115"
+        "timestamp": "2025-04-01T14:11:31.224666892"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml
index a80302fcf68f..7aa06d0f7a00 100644
--- a/modules/nf-core/bcftools/stats/environment.yml
+++ b/modules/nf-core/bcftools/stats/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::bcftools=1.21
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf
index 20e5da77133e..fb556e0aa5b6 100644
--- a/modules/nf-core/bcftools/stats/main.nf
+++ b/modules/nf-core/bcftools/stats/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_STATS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta),  path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap
index cd8cff6d2b0f..c771a055b9a8 100644
--- a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2 - vcf_gz - reference": {
         "content": [
             [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
+                "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  --fasta-ref genome.fasta test.vcf.gz",
                 "#",
                 "# Definition of sets:",
@@ -11,15 +11,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:14:35.506777837"
+        "timestamp": "2025-04-01T14:12:00.636338532"
     },
     "sarscov2 - vcf_gz - exons": {
         "content": [
             [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
+                "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  --exons exons.tsv.gz test.vcf.gz",
                 "#",
                 "# Definition of sets:",
@@ -28,27 +28,27 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:14:30.57486244"
+        "timestamp": "2025-04-01T14:11:56.472662944"
     },
     "versions": {
         "content": [
             [
-                "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a"
+                "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:16:27.637515559"
+        "timestamp": "2025-04-01T14:11:38.17663878"
     },
     "sarscov2 - vcf_gz - targets": {
         "content": [
             [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
+                "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  --targets-file test2.targets.tsv.gz test.vcf.gz",
                 "#",
                 "# Definition of sets:",
@@ -57,34 +57,34 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:14:25.732997442"
+        "timestamp": "2025-04-01T14:11:49.263021261"
     },
     "regions_versions": {
         "content": [
             [
-                "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a"
+                "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:16:32.559884458"
+        "timestamp": "2025-04-01T14:11:45.263363932"
     },
     "targets_versions": {
         "content": [
             [
-                "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a"
+                "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:16:37.512009805"
+        "timestamp": "2025-04-01T14:11:49.260150422"
     },
     "sarscov2 - vcf_gz - stub": {
         "content": [
@@ -98,7 +98,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a"
+                    "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4"
                 ],
                 "stats": [
                     [
@@ -109,44 +109,44 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a"
+                    "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-03T11:57:09.614976125"
+        "timestamp": "2025-04-01T14:12:07.469893476"
     },
     "exon_versions": {
         "content": [
             [
-                "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a"
+                "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:16:42.347397266"
+        "timestamp": "2025-04-01T14:11:56.46980859"
     },
     "ref_versions": {
         "content": [
             [
-                "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a"
+                "versions.yml:md5,d8ba64d31cb19c789af4726840d8f5f4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:16:47.26823622"
+        "timestamp": "2025-04-01T14:12:00.633746007"
     },
     "sarscov2 - vcf_gz": {
         "content": [
             [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
+                "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  test.vcf.gz",
                 "#",
                 "# Definition of sets:",
@@ -155,15 +155,15 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:16:27.670416598"
+        "timestamp": "2025-04-01T14:11:38.184907984"
     },
     "sarscov2 - vcf_gz - regions": {
         "content": [
             [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
+                "# This file was produced by bcftools stats (1.21+htslib-1.21) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  --regions-file test3.vcf.gz test.vcf.gz",
                 "#",
                 "# Definition of sets:",
@@ -172,9 +172,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T18:14:20.759094062"
+        "timestamp": "2025-04-01T14:11:45.266296334"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml
index b276efd90d30..557488607c73 100644
--- a/modules/nf-core/bcftools/view/environment.yml
+++ b/modules/nf-core/bcftools/view/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  - bioconda::bcftools=1.21
diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf
index aa197b090fe9..5ef5d1bc6b98 100644
--- a/modules/nf-core/bcftools/view/main.nf
+++ b/modules/nf-core/bcftools/view/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_VIEW {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test.snap b/modules/nf-core/bcftools/view/tests/main.nf.test.snap
index fec22e3664b4..93d9adb66ab9 100644
--- a/modules/nf-core/bcftools/view/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/view/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
                 ],
                 "csi": [
                     [
@@ -48,15 +48,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:14:38.717458272"
+        "timestamp": "2025-04-01T14:12:56.166195802"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": {
         "content": [
@@ -82,14 +82,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:13:44.760671384"
+        "timestamp": "2025-04-01T14:12:33.048845065"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": {
         "content": [
@@ -116,7 +116,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
                 ],
                 "csi": [
                     [
@@ -140,15 +140,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-04T16:06:21.669668533"
+        "timestamp": "2025-04-01T14:12:52.003188711"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": {
         "content": [
@@ -175,7 +175,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
                 ],
                 "csi": [
                     
@@ -199,15 +199,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:14:53.026083914"
+        "timestamp": "2025-04-01T14:13:03.303865495"
     },
     "sarscov2 - [vcf, tbi], vcf, tsv, []": {
         "content": [
@@ -221,27 +221,27 @@
                 ]
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:15:14.663512924"
+        "timestamp": "2025-04-01T14:12:40.727725444"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
             "out.vcf",
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:15:19.723448323"
+        "timestamp": "2025-04-01T14:12:47.850438431"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": {
         "content": [
@@ -267,14 +267,14 @@
                 
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T08:24:36.358469315"
+        "timestamp": "2025-04-01T14:12:21.639961317"
     },
     "sarscov2 - [vcf, tbi], [], [], []": {
         "content": [
@@ -288,14 +288,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-31T15:15:09.588867653"
+        "timestamp": "2025-04-01T14:12:14.557692028"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": {
         "content": [
@@ -321,13 +321,13 @@
                 
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,dcf736f3b92fe7943416d890ed15521e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-06-05T12:13:33.834986869"
+        "timestamp": "2025-04-01T14:12:25.812993907"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/blast/updateblastdb/environment.yml b/modules/nf-core/blast/updateblastdb/environment.yml
index 968930b63d97..31e790fabc7e 100644
--- a/modules/nf-core/blast/updateblastdb/environment.yml
+++ b/modules/nf-core/blast/updateblastdb/environment.yml
@@ -1,7 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::blast=2.15.0
+  - bioconda::blast=2.16.0
diff --git a/modules/nf-core/blast/updateblastdb/main.nf b/modules/nf-core/blast/updateblastdb/main.nf
index 765ff5eb8353..8dbee12f558c 100644
--- a/modules/nf-core/blast/updateblastdb/main.nf
+++ b/modules/nf-core/blast/updateblastdb/main.nf
@@ -4,8 +4,8 @@ process BLAST_UPDATEBLASTDB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1':
-        'biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.16.0--h66d330f_4':
+        'biocontainers/blast:2.16.0--h66d330f_4' }"
 
     input:
     tuple val(meta), val(name)
diff --git a/modules/nf-core/blast/updateblastdb/tests/main.nf.test.snap b/modules/nf-core/blast/updateblastdb/tests/main.nf.test.snap
index 10ef43cd236a..88301dde3589 100644
--- a/modules/nf-core/blast/updateblastdb/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/updateblastdb/tests/main.nf.test.snap
@@ -2,37 +2,37 @@
     "versions_stub": {
         "content": [
             [
-                "versions.yml:md5,6050ce42d119aa1b2b529a9e2d95c990"
+                "versions.yml:md5,3c53c59220b9d187aa3cdc74287fe76a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-10T17:26:53.519592642"
+        "timestamp": "2025-04-01T12:46:53.571738436"
     },
     "versions_decompressed": {
         "content": [
             [
-                "versions.yml:md5,6050ce42d119aa1b2b529a9e2d95c990"
+                "versions.yml:md5,3c53c59220b9d187aa3cdc74287fe76a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-10T17:26:46.433343719"
+        "timestamp": "2025-04-01T12:46:42.933848568"
     },
     "versions_compressed": {
         "content": [
             [
-                "versions.yml:md5,6050ce42d119aa1b2b529a9e2d95c990"
+                "versions.yml:md5,3c53c59220b9d187aa3cdc74287fe76a"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-10T17:25:51.663130031"
+        "timestamp": "2025-04-01T12:45:46.532402897"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test
index 0fbcdc4657b2..ee94c19c911c 100644
--- a/modules/nf-core/bowtie2/build/tests/main.nf.test
+++ b/modules/nf-core/bowtie2/build/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/cellrangerarc/count/main.nf b/modules/nf-core/cellrangerarc/count/main.nf
index e5ce922590cb..f6e94a5c8e92 100644
--- a/modules/nf-core/cellrangerarc/count/main.nf
+++ b/modules/nf-core/cellrangerarc/count/main.nf
@@ -4,7 +4,7 @@ process CELLRANGERARC_COUNT {
 
     container "nf-core/cellranger-arc:2.0.2"
 
-    // Exit if running this module with -profile conda / -profile mamba
+    // Exit if running this module with -profile conda / -profile mamba 
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "CELLRANGERARC_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
diff --git a/modules/nf-core/cellrangerarc/count/tests/main.nf.test b/modules/nf-core/cellrangerarc/count/tests/main.nf.test
new file mode 100644
index 000000000000..8fad46075289
--- /dev/null
+++ b/modules/nf-core/cellrangerarc/count/tests/main.nf.test
@@ -0,0 +1,171 @@
+nextflow_process {
+
+    name "Test Process CELLRANGERARC_COUNT"
+    script "../main.nf"
+    process "CELLRANGERARC_COUNT"
+   
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cellrangerarc"
+    tag "cellrangerarc/mkref"
+    tag "cellrangerarc/count"
+    tag "unzip"
+   
+    setup {
+        run("UNZIP") {
+            script "../../../unzip/main.nf"
+
+            process {
+                """
+                input[0] = [[],file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.fa.gz',checkIfExists:true)]
+                """
+            }
+        }
+        run("CELLRANGERARC_MKREF") {
+            script "../../mkref/main.nf"
+
+            process {
+                """
+                input[0] = UNZIP.out.unzipped_archive.map{it[1]}+"/chr19.fa"
+                input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.filtered.gtf.gz',checkIfExists:true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_motifs.txt',checkIfExists:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json',checkIfExists:true)
+                input[4] = "cellrangerarc_reference"
+                """
+            }
+        }
+    }
+    test("test_cellrangerarc_count") {
+
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [[id:'test'],['gex','atac'],['SRR18907480_chr19_sub','SRR18907481_chr19_sub'],
+                    [file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz',checkIfExists:true),
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz',checkIfExists:true),
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz',checkIfExists:true),
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz',checkIfExists:true),
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz',checkIfExists:true)
+                    ]
+                    ]
+                input[1] = CELLRANGERARC_MKREF.out.reference
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    def all_files = process.out.outs[0][1]
+
+                    def stable_file_names = [
+                        'analysis/clustering/atac/graphclust/clusters.csv',
+                        'analysis/clustering/atac/graphclust/differential_accessibility.csv',
+                        'analysis/clustering/atac/graphclust/differential_expression.csv',
+                        'analysis/clustering/atac/kmeans_2_clusters/clusters.csv',
+                        'analysis/clustering/atac/kmeans_2_clusters/differential_accessibility.csv',
+                        'analysis/clustering/atac/kmeans_2_clusters/differential_expression.csv',
+                        'analysis/clustering/atac/kmeans_3_clusters/clusters.csv',
+                        'analysis/clustering/atac/kmeans_3_clusters/differential_accessibility.csv',
+                        'analysis/clustering/atac/kmeans_3_clusters/differential_expression.csv',
+                        'analysis/clustering/atac/kmeans_4_clusters/clusters.csv',
+                        'analysis/clustering/atac/kmeans_4_clusters/differential_accessibility.csv',
+                        'analysis/clustering/atac/kmeans_4_clusters/differential_expression.csv',
+                        'analysis/clustering/atac/kmeans_5_clusters/clusters.csv',
+                        'analysis/clustering/atac/kmeans_5_clusters/differential_accessibility.csv',
+                        'analysis/clustering/atac/kmeans_5_clusters/differential_expression.csv',
+                        'analysis/clustering/gex/graphclust/clusters.csv',
+                        'analysis/clustering/gex/graphclust/differential_accessibility.csv',
+                        'analysis/clustering/gex/graphclust/differential_expression.csv',
+                        'analysis/clustering/gex/kmeans_2_clusters/clusters.csv',
+                        'analysis/clustering/gex/kmeans_2_clusters/differential_accessibility.csv',
+                        'analysis/clustering/gex/kmeans_2_clusters/differential_expression.csv',
+                        'analysis/clustering/gex/kmeans_3_clusters/clusters.csv',
+                        'analysis/clustering/gex/kmeans_3_clusters/differential_accessibility.csv',
+                        'analysis/clustering/gex/kmeans_3_clusters/differential_expression.csv',
+                        'analysis/clustering/gex/kmeans_4_clusters/clusters.csv',
+                        'analysis/clustering/gex/kmeans_4_clusters/differential_accessibility.csv',
+                        'analysis/clustering/gex/kmeans_4_clusters/differential_expression.csv',
+                        'analysis/clustering/gex/kmeans_5_clusters/clusters.csv',
+                        'analysis/clustering/gex/kmeans_5_clusters/differential_accessibility.csv',
+                        'analysis/clustering/gex/kmeans_5_clusters/differential_expression.csv',
+                        'analysis/dimensionality_reduction/atac/lsa_components.csv',
+                        'analysis/dimensionality_reduction/atac/lsa_dispersion.csv',
+                        'analysis/dimensionality_reduction/atac/lsa_features_selected.csv',
+                        'analysis/dimensionality_reduction/atac/lsa_projection.csv',
+                        'analysis/dimensionality_reduction/atac/lsa_variance.csv',
+                        'analysis/dimensionality_reduction/atac/tsne_projection.csv',
+                        'analysis/dimensionality_reduction/atac/umap_projection.csv',
+                        'analysis/dimensionality_reduction/gex/pca_components.csv',
+                        'analysis/dimensionality_reduction/gex/pca_dispersion.csv',
+                        'analysis/dimensionality_reduction/gex/pca_features_selected.csv',
+                        'analysis/dimensionality_reduction/gex/pca_projection.csv',
+                        'analysis/dimensionality_reduction/gex/pca_variance.csv',
+                        'analysis/dimensionality_reduction/gex/tsne_projection.csv',
+                        'analysis/dimensionality_reduction/gex/umap_projection.csv',
+                        'analysis/feature_linkage/feature_linkage.bedpe',
+                        'analysis/tf_analysis/filtered_tf_bc_matrix/barcodes.tsv.gz',
+                        'analysis/tf_analysis/filtered_tf_bc_matrix/matrix.mtx.gz',
+                        'analysis/tf_analysis/filtered_tf_bc_matrix/motifs.tsv',
+                        'analysis/tf_analysis/peak_motif_mapping.bed',
+                        'atac_cut_sites.bigwig',
+                        'atac_peak_annotation.tsv',
+                        'filtered_feature_bc_matrix/barcodes.tsv.gz',
+                        'filtered_feature_bc_matrix/features.tsv.gz',
+                        'filtered_feature_bc_matrix/matrix.mtx.gz',
+                        'gex_molecule_info.h5',
+                        'gex_possorted_bam.bam',
+                        'gex_possorted_bam.bam.bai',
+                        'per_barcode_metrics.csv',
+                        'raw_feature_bc_matrix/barcodes.tsv.gz',
+                        'raw_feature_bc_matrix/features.tsv.gz',
+                        'raw_feature_bc_matrix/matrix.mtx.gz',
+                        'summary.csv',
+                    ]
+
+                    def stable_files = all_files.findAll { file ->
+                        // Check if the file path ends with any of the stable file paths
+                        return stable_file_names.any { stable_path ->
+                            file.toString().endsWith(stable_path)
+                        }
+                    }.toSorted()
+
+                    assert snapshot(
+                        stable_files,
+                        process.out.versions[0]
+                    ).match()
+
+                    def unstable_file_names = [
+                        'analysis/feature_linkage/feature_linkage_matrix.h5',
+                        'analysis/tf_analysis/filtered_tf_bc_matrix.h5',
+                        'atac_fragments.tsv.gz',
+                        'atac_fragments.tsv.gz.tbi',
+                        'atac_peaks.bed',
+                        'atac_possorted_bam.bam',
+                        'atac_possorted_bam.bam.bai',
+                        'cloupe.cloupe',
+                        'filtered_feature_bc_matrix.h5',
+                        'raw_feature_bc_matrix.h5',
+                        'web_summary.html'
+                    ]
+
+                    def unstable_files = all_files.findAll { file ->
+                        return unstable_file_names.any { unstable_path ->
+                            file.toString().endsWith(unstable_path)
+                        }
+                    }.toSorted()
+
+                    unstable_files.each { filePath ->
+                        def fileObj = file(filePath)
+                        assert fileObj.exists(): "File ${filePath} does not exist"
+                    }
+                }
+            )
+        }
+    }
+// No stub test, as the stub test for `UNZIP` doesn't actually extract the archive.
+// This breaks the downstream stub tests as a fasta file is required.
+}
diff --git a/modules/nf-core/cellrangerarc/count/tests/main.nf.test.snap b/modules/nf-core/cellrangerarc/count/tests/main.nf.test.snap
new file mode 100644
index 000000000000..43125f2f00df
--- /dev/null
+++ b/modules/nf-core/cellrangerarc/count/tests/main.nf.test.snap
@@ -0,0 +1,76 @@
+{
+    "test_cellrangerarc_count": {
+        "content": [
+            [
+                "clusters.csv:md5,ed29b219ca3b79305129aea2d38ca60e",
+                "differential_accessibility.csv:md5,90e3e1001432bd1f94f53f39ae86971c",
+                "differential_expression.csv:md5,2806595b0c66af8407977b6ea57e30a3",
+                "clusters.csv:md5,35232075d0184cc6a31178ed58176bbe",
+                "differential_accessibility.csv:md5,0c597e33c58aac61a54e71c0ca3d1343",
+                "differential_expression.csv:md5,e77580db30873fba52bf4490f752ed22",
+                "clusters.csv:md5,127636548ad77bfa2646cbf62209e73b",
+                "differential_accessibility.csv:md5,9d1efbb7209c95a6f7714b43aca22130",
+                "differential_expression.csv:md5,24a85767ec0013a9f444bed5b23fb7f2",
+                "clusters.csv:md5,c84df7cc5cb684dd4a431915df0b58b2",
+                "differential_accessibility.csv:md5,2492068224aba9a65f860b6fb3464056",
+                "differential_expression.csv:md5,e02a8c8e3bc1d924357b46af2da76a6b",
+                "clusters.csv:md5,fcbbc4f29456778935fbbf4dc52791ea",
+                "differential_accessibility.csv:md5,630f412020f85765b2a32ac689701ce5",
+                "differential_expression.csv:md5,0aae96dbf649f0bc738f5d2c19e2be76",
+                "clusters.csv:md5,6cd4c2b06047c99cee59548c9b3000ac",
+                "differential_accessibility.csv:md5,08fc89ad11d1834cab677390f385a88a",
+                "differential_expression.csv:md5,6e97ced39f84b02f843f0b757b02f100",
+                "clusters.csv:md5,cd135bf9e9b5aa69abe95d5356aec96c",
+                "differential_accessibility.csv:md5,9ef66432c3f66f2190ff936324091e9f",
+                "differential_expression.csv:md5,223e516ce7ddf219575a32a60217e83d",
+                "clusters.csv:md5,ae9c24a834f1863a8faf03b3b4bdf74a",
+                "differential_accessibility.csv:md5,84bf1b3b3c90abdd92a817cc5a9d2ee8",
+                "differential_expression.csv:md5,8b0ec69f3cd0d3156d6def50cdde4340",
+                "clusters.csv:md5,aceb697994f98ee50b4d3db8e12e2a3a",
+                "differential_accessibility.csv:md5,05f0b3a10ce71d2fbafc6c9b74acf969",
+                "differential_expression.csv:md5,7b339771b1731b9cff2c52ac4fc632ce",
+                "clusters.csv:md5,243233d51193e6ce3127ed5ef8a08daf",
+                "differential_accessibility.csv:md5,25deefdff4c870e52c84f97cc4b9d5d2",
+                "differential_expression.csv:md5,b70730d7301cba11c46297d08b81677d",
+                "lsa_components.csv:md5,c3a48d3849f6b5e268bcb16b4d3db7ec",
+                "lsa_dispersion.csv:md5,1bdae634bd63d044dcfd8ae821b3744c",
+                "lsa_features_selected.csv:md5,b4e3cc5cac26dc6df059c1b8e38e72a8",
+                "lsa_projection.csv:md5,3bce47a5a0e8dc0cb24c2ecbba5c745b",
+                "lsa_variance.csv:md5,ff92c64ec140084673fd7ec48ce48993",
+                "tsne_projection.csv:md5,b0ff0a327a7cad898087c169b9815bab",
+                "umap_projection.csv:md5,8a34ad7bcf4ae7d14ad8f451acb4a12e",
+                "pca_components.csv:md5,82a4384a22390821cbfe06b2de9e9b4d",
+                "pca_dispersion.csv:md5,a6c8d15062a67bf828c1b58d1bc1eff8",
+                "pca_features_selected.csv:md5,34acd3e8d57f68bf592856c0c69847e7",
+                "pca_projection.csv:md5,6a2bf5e268da6705b92ec02309b3f61e",
+                "pca_variance.csv:md5,060e80415e690a7bfc9cd385c929842f",
+                "tsne_projection.csv:md5,aa42abe3c868c7d0e35628acf1a24966",
+                "umap_projection.csv:md5,34acdb54ff9f9c8b7d7f91a625450294",
+                "feature_linkage.bedpe:md5,4a92b2e49591c21a3d08602235e6ef7a",
+                "barcodes.tsv.gz:md5,1b2010b38c2de59bea1b71d374114919",
+                "matrix.mtx.gz:md5,2627809b0951961282c3b31fb83d7f1b",
+                "motifs.tsv:md5,9a397341713d07560937054df442afcb",
+                "peak_motif_mapping.bed:md5,b1d02a287485989ca294284bd95ad572",
+                "atac_cut_sites.bigwig:md5,03e0c63674192256d55a3c117fff66ee",
+                "atac_peak_annotation.tsv:md5,f4770b4197ff32c74bd206476f1f0dba",
+                "barcodes.tsv.gz:md5,1b2010b38c2de59bea1b71d374114919",
+                "features.tsv.gz:md5,9a315f46dbf99b9120527df78fd7e081",
+                "matrix.mtx.gz:md5,2304085aaac98027cf9241a3b2593760",
+                "gex_molecule_info.h5:md5,f1ab414eb8b8da017c974d7109f5e7ca",
+                "gex_possorted_bam.bam:md5,8455846fa1aa417e4252bd09584d1098",
+                "gex_possorted_bam.bam.bai:md5,444fb175b75d0e22c8e14724b7790e34",
+                "per_barcode_metrics.csv:md5,055ddb433b94d44efa0113a1db84a63d",
+                "barcodes.tsv.gz:md5,4e020c4c968100a61a542c0d6e56e5f5",
+                "features.tsv.gz:md5,9a315f46dbf99b9120527df78fd7e081",
+                "matrix.mtx.gz:md5,743fc9d85f85cd2e5a40654d3ae2e3e4",
+                "summary.csv:md5,7641192d4cc0c6072dc447a46d5f89a2"
+            ],
+            "versions.yml:md5,dc627e4bae7ded9a34b7e8f52b4b903d"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-03T18:30:31.250399555"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/cellrangerarc/count/tests/nextflow.config b/modules/nf-core/cellrangerarc/count/tests/nextflow.config
new file mode 100644
index 000000000000..1ff901dd7aca
--- /dev/null
+++ b/modules/nf-core/cellrangerarc/count/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+	withName: 'CELLRANGERARC_COUNT': {
+		ext.args = params.module_args
+	}
+}
diff --git a/modules/nf-core/cellrangerarc/mkref/main.nf b/modules/nf-core/cellrangerarc/mkref/main.nf
index b030ae921d37..13b5d2f13bbf 100644
--- a/modules/nf-core/cellrangerarc/mkref/main.nf
+++ b/modules/nf-core/cellrangerarc/mkref/main.nf
@@ -4,11 +4,6 @@ process CELLRANGERARC_MKREF {
 
     container "nf-core/cellranger-arc:2.0.2"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGERARC_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path fasta
     path gtf
@@ -25,6 +20,10 @@ process CELLRANGERARC_MKREF {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "CELLRANGERARC_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def fast_name = fasta.name
     def gtf_name = gtf.name
     def motifs_name = motifs.name
@@ -82,4 +81,20 @@ process CELLRANGERARC_MKREF {
         cellrangerarc: \$(echo \$( cellranger-arc --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
     END_VERSIONS
     """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "CELLRANGERARC_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    """
+    mkdir -p "${reference_name}/"
+    touch config
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cellrangerarc: \$(echo \$( cellranger-arc --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/cellrangerarc/mkref/tests/main.nf.test b/modules/nf-core/cellrangerarc/mkref/tests/main.nf.test
new file mode 100644
index 000000000000..02d2abdee35d
--- /dev/null
+++ b/modules/nf-core/cellrangerarc/mkref/tests/main.nf.test
@@ -0,0 +1,91 @@
+nextflow_process {
+
+    name "Test Process CELLRANGERARC_MKREF"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "CELLRANGERARC_MKREF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cellrangerarc"
+    tag "cellrangerarc/mkref"
+    tag "unzip"
+
+    setup {
+            run("UNZIP") {
+                script "../../../unzip/main.nf"
+
+                process {
+                    """
+                    input[0] = [[],file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.fa.gz',checkIfExists:true)]
+                    """
+            }
+        }
+    }
+    test("mouse - fa.gz") {
+
+        when {
+            process {
+                """
+                input[0] = UNZIP.out.unzipped_archive.map{it[1]}+"/chr19.fa"
+                input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.filtered.gtf.gz',checkIfExists:true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_motifs.txt',checkIfExists:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json',checkIfExists:true)
+                input[4] = "cellrangerarc_reference"
+                """
+            }
+        }
+        then {
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.config,
+                    process.out.versions,
+                    path( "${outputDir}/cellrangerarc_reference/fasta/"                        ),
+                    path( "${outputDir}/cellrangerarc_reference/genes/"                        ),
+                    path( "${outputDir}/cellrangerarc_reference/regions"                       ),
+                    path( "${outputDir}/cellrangerarc_reference/reference.json"                ),
+                    path( "${outputDir}/cellrangerarc_reference/star/chrLength.txt"            ),
+                    path( "${outputDir}/cellrangerarc_reference/star/chrName.txt"              ),
+                    path( "${outputDir}/cellrangerarc_reference/star/chrNameLength.txt"        ),
+                    path( "${outputDir}/cellrangerarc_reference/star/chrStart.txt"             ),
+                    path( "${outputDir}/cellrangerarc_reference/star/exonGeTrInfo.tab"         ),
+                    path( "${outputDir}/cellrangerarc_reference/star/exonInfo.tab"             ),
+                    path( "${outputDir}/cellrangerarc_reference/star/geneInfo.tab"             ),
+                    path( "${outputDir}/cellrangerarc_reference/star/Genome"                   ),
+                    path( "${outputDir}/cellrangerarc_reference/star/SA"                       ),
+                    path( "${outputDir}/cellrangerarc_reference/star/SAindex"                  ),
+                    path( "${outputDir}/cellrangerarc_reference/star/sjdbInfo.txt"             ),
+                    path( "${outputDir}/cellrangerarc_reference/star/sjdbList.fromGTF.out.tab" ),
+                    path( "${outputDir}/cellrangerarc_reference/star/sjdbList.out.tab"         ),
+                    path( "${outputDir}/cellrangerarc_reference/star/transcriptInfo.tab"       ),
+                ).match() }
+            )
+        }
+    }
+
+    test("mouse - fa.gz - stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = UNZIP.out.unzipped_archive.map{it[1]}+"/chr19.fa"
+                input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.filtered.gtf.gz',checkIfExists:true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_motifs.txt',checkIfExists:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json',checkIfExists:true)
+                input[4] = "cellrangerarc_reference"
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/cellrangerarc/mkref/tests/main.nf.test.snap b/modules/nf-core/cellrangerarc/mkref/tests/main.nf.test.snap
new file mode 100644
index 000000000000..17ee0a90435e
--- /dev/null
+++ b/modules/nf-core/cellrangerarc/mkref/tests/main.nf.test.snap
@@ -0,0 +1,89 @@
+{
+    "mouse - fa.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        
+                    ]
+                ],
+                "1": [
+                    "config:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "versions.yml:md5,4a1d57a87e4b95fa5fd703d4536bedbd"
+                ],
+                "config": [
+                    "config:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "reference": [
+                    [
+                        
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4a1d57a87e4b95fa5fd703d4536bedbd"
+                ]
+            },
+            [
+                {
+                    "CELLRANGERARC_MKREF": {
+                        "cellrangerarc": "2.0.2"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T09:17:19.337666684"
+    },
+    "mouse - fa.gz": {
+        "content": [
+            [
+                "config:md5,be9df01d35e426f4f37bdca2c779e199"
+            ],
+            [
+                "versions.yml:md5,4a1d57a87e4b95fa5fd703d4536bedbd"
+            ],
+            [
+                "genome.fa:md5,dd9375c0cfa5de18757a0608411ff608",
+                "genome.fa.amb:md5,1b4fb43678899d6115d37d88f22552ad",
+                "genome.fa.ann:md5,4df1dc4bd46b294e1e1343dc0ab646ef",
+                "genome.fa.bwt:md5,64d2ab05657806c66fb0e0d1ea7fc4d1",
+                "genome.fa.fai:md5,291a00d5431e0f97c356c272d201d8bd",
+                "genome.fa.pac:md5,7554f21668cd8efc77f1272b95550cc3",
+                "genome.fa.sa:md5,7d4b562f369d65ad60a889f74609f330"
+            ],
+            [
+                "genes.gtf.gz:md5,29ea9f8629c84868b4b0ce5cd4f57632"
+            ],
+            [
+                "motifs.pfm:md5,294d4041e4ffd4c633376c2b9d180ac0",
+                "transcripts.bed:md5,bc5cfb75dc1795cfc2caeddfc15aaa30",
+                "tss.bed:md5,6aa464a762cab3ca3bf004dd6f35de8e"
+            ],
+            "reference.json:md5,1ff977fa99515695d81b8da012569901",
+            "chrLength.txt:md5,263f433d64f5f9f3181ed90542735474",
+            "chrName.txt:md5,255cdc5fefdc3ff84cfe3f3270ab8fed",
+            "chrNameLength.txt:md5,bb9ac7f24e6c1c6ea0677f825858449a",
+            "chrStart.txt:md5,fba9f49cedf08a4136244d4b9b776c01",
+            "exonGeTrInfo.tab:md5,4fb4acda70869b18296f8ce9c6a297db",
+            "exonInfo.tab:md5,e2f4405c0cbf847580791f2e9954f936",
+            "geneInfo.tab:md5,786000c34020b0b39e4ab6b9b3e4d922",
+            "Genome:md5,4664d17f3cbcde9859f1af9fac08f9ed",
+            "SA:md5,3c73b38e44260c9a591e74f5f1dfec87",
+            "SAindex:md5,c1ba6a91058b189bffa7a56592635f23",
+            "sjdbInfo.txt:md5,17bd31bf73ea326f7befac8a57dc1780",
+            "sjdbList.fromGTF.out.tab:md5,23c67498223466c717f6f901ff9df9a4",
+            "sjdbList.out.tab:md5,6923d3e29967b2f3faad78960101a2a6",
+            "transcriptInfo.tab:md5,b3b9193220aaa3fbf63a49148ef150e0"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T09:17:00.006663869"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/cellrangerarc/mkref/tests/nextflow.config b/modules/nf-core/cellrangerarc/mkref/tests/nextflow.config
new file mode 100644
index 000000000000..c748938d1773
--- /dev/null
+++ b/modules/nf-core/cellrangerarc/mkref/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: CELLRANGERARC_MKREF {
+        publishDir = [ path: { "output" } ]
+    }
+}
diff --git a/modules/nf-core/clair3/main.nf b/modules/nf-core/clair3/main.nf
index d893ae133de4..22007298bb1d 100644
--- a/modules/nf-core/clair3/main.nf
+++ b/modules/nf-core/clair3/main.nf
@@ -8,7 +8,7 @@ process CLAIR3 {
         'biocontainers/clair3:1.0.10--py39hd649744_1' }"
 
     input:
-    tuple val(meta), path(bam), path(bai), path(model), val(platform)
+    tuple val(meta), path(bam), path(bai), val(packaged_model), path(user_model), val(platform)
     tuple val(meta2), path(reference)
     tuple val(meta3), path(index)
 
@@ -23,6 +23,21 @@ process CLAIR3 {
     task.ext.when == null || task.ext.when
 
     script:
+    def model = ""
+    if (!user_model) {
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+            model = "\${CONDA_PREFIX}/bin/models/${packaged_model}"
+        }
+        else {
+            model = "/usr/local/bin/models/$packaged_model"
+        }
+    }
+    if (!packaged_model) {
+        model = "$user_model"
+    }
+    if (packaged_model && user_model) {
+        error "Two models specified $user_model and $packaged_model, specify one of them."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
diff --git a/modules/nf-core/clair3/meta.yml b/modules/nf-core/clair3/meta.yml
index bc12fd627f06..5ba5105bab7c 100644
--- a/modules/nf-core/clair3/meta.yml
+++ b/modules/nf-core/clair3/meta.yml
@@ -39,9 +39,13 @@ input:
       type: file
       description: BAM index file
       pattern: "*.bai"
-  - model:
+  - packaged_model:
+      type: string
+      description: string containing the name of a prepackaged Clair3 model
+        full list of models and their descriptions is provided at https://github.com/HKU-BAL/Clair3?tab=readme-ov-file#pre-trained-models
+  - user_model:
       type: directory
-      description: collection of files used in a trained Clair3 model
+      description: directory containing Clair3 model files
   - platform:
       type: string
       description: val in ['hifi','ont', 'ilmn'] to indicate pacbio, ONT, or illumina
diff --git a/modules/nf-core/clair3/tests/main.nf.test b/modules/nf-core/clair3/tests/main.nf.test
index a69d417b65b7..8e9c8cc379ab 100644
--- a/modules/nf-core/clair3/tests/main.nf.test
+++ b/modules/nf-core/clair3/tests/main.nf.test
@@ -21,8 +21,8 @@ nextflow_process {
                 """
             }
         }
-       }
-    test("sarscov2 - bam") {
+    }
+    test("sarscov2 - bam - user_model") {
 
         when {
             process {
@@ -32,8 +32,50 @@ nextflow_process {
                     [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    [],
+                ])
+                .join(UNTAR.out.untar)
+                .combine(Channel.of(['hifi']))
+                input[1] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                input[2] = [
+                    [ id: 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { file(it[1]).getName() },
+                    process.out.tbi.collect { file(it[1]).getName() },
+                    process.out.versions,
+                    process.out.phased_vcf.collect { file(it[1]).getName() },
+                    process.out.phased_tbi.collect { file(it[1]).getName() })
+                    .match()}
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - packaged_model") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    'hifi_revio',
+                    [],
+                    'hifi',
                 ])
-                .join(UNTAR.out.untar).combine(Channel.of(['hifi']))
                 input[1] = [
                     [ id:'test'],
                     file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
@@ -50,16 +92,51 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                                process.out.vcf.collect { file(it[1]).getName() },
-                                process.out.tbi.collect { file(it[1]).getName() },
-                                process.out.versions,
-                                process.out.phased_vcf.collect { file(it[1]).getName() },
-                                process.out.phased_tbi.collect { file(it[1]).getName() }).match()}
+                    process.out.vcf.collect { file(it[1]).getName() },
+                    process.out.tbi.collect { file(it[1]).getName() },
+                    process.out.versions,
+                    process.out.phased_vcf.collect { file(it[1]).getName() },
+                    process.out.phased_tbi.collect { file(it[1]).getName() })
+                    .match()}
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - both") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    ['hifi_revio'],
+                ])
+                .join(UNTAR.out.untar)
+                .combine(Channel.of(['hifi']))
+                input[1] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                input[2] = [
+                    [ id: 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed }
             )
         }
 
     }
 
+
     test("sarscov2 - bam - stub") {
 
         options "-stub"
@@ -72,8 +149,10 @@ nextflow_process {
                     [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    [],
                 ])
-                .join(UNTAR.out.untar).combine(Channel.of(['hifi']))
+                .join(UNTAR.out.untar)
+                .combine(Channel.of(['hifi']))
                 input[1] = [
                     [ id:'test'],
                     file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
@@ -90,12 +169,12 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                                process.out.vcf,
-                                process.out.tbi,
-                                process.out.phased_vcf,
-                                process.out.phased_tbi,
-                                process.out.versions,
-                                ).match()}
+                        process.out.vcf,
+                        process.out.tbi,
+                        process.out.phased_vcf,
+                        process.out.phased_tbi,
+                        process.out.versions)
+                        .match()}
             )
         }
 
diff --git a/modules/nf-core/clair3/tests/main.nf.test.snap b/modules/nf-core/clair3/tests/main.nf.test.snap
index fe9e76f80c0e..e9b68be83826 100644
--- a/modules/nf-core/clair3/tests/main.nf.test.snap
+++ b/modules/nf-core/clair3/tests/main.nf.test.snap
@@ -47,9 +47,9 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-17T09:56:09.775735"
+        "timestamp": "2025-04-04T09:30:51.327348"
     },
-    "sarscov2 - bam": {
+    "sarscov2 - bam - packaged_model": {
         "content": [
             [
                 "merge_output.vcf.gz"
@@ -71,6 +71,30 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-14T17:16:02.057639"
+        "timestamp": "2025-04-04T09:30:16.61651"
+    },
+    "sarscov2 - bam - user_model": {
+        "content": [
+            [
+                "merge_output.vcf.gz"
+            ],
+            [
+                "merge_output.vcf.gz.tbi"
+            ],
+            [
+                "versions.yml:md5,10928c13418eced076964d86249aeaf8"
+            ],
+            [
+                
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-04T09:29:58.640181"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf
index 98a2db223779..652cdceefaaa 100644
--- a/modules/nf-core/damageprofiler/main.nf
+++ b/modules/nf-core/damageprofiler/main.nf
@@ -23,7 +23,7 @@ process DAMAGEPROFILER {
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
-    def reference    = fasta ? "-r $fasta" : ""
+    def reference    = fasta       ? "-r $fasta"        : ""
     def species_list = specieslist ? "-sf $specieslist" : ""
     """
     damageprofiler \\
@@ -38,4 +38,36 @@ process DAMAGEPROFILER {
         damageprofiler: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p $prefix
+
+    touch $prefix/3pGtoA_freq.txt
+    touch $prefix/3p_freq_misincorporations.txt
+    touch $prefix/5pCtoT_freq.txt
+    touch $prefix/5p_freq_misincorporations.txt
+    touch $prefix/DNA_comp_genome.txt
+    touch $prefix/DNA_composition_sample.txt
+    touch $prefix/DamagePlot.pdf
+    touch $prefix/DamagePlot_five_prime.svg
+    touch $prefix/DamagePlot_three_prime.svg
+    touch $prefix/DamageProfiler.log
+    touch $prefix/Length_plot.pdf
+    touch $prefix/Length_plot_combined_data.svg
+    touch $prefix/Length_plot_forward_reverse_separated.svg
+    touch $prefix/dmgprof.json
+    touch $prefix/editDistance.txt
+    touch $prefix/edit_distance.pdf
+    touch $prefix/edit_distance.svg
+    touch $prefix/lgdistribution.txt
+    touch $prefix/misincorporation.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        damageprofiler: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/damageprofiler/meta.yml b/modules/nf-core/damageprofiler/meta.yml
index 0c3360e893bb..01e4171fbde8 100644
--- a/modules/nf-core/damageprofiler/meta.yml
+++ b/modules/nf-core/damageprofiler/meta.yml
@@ -32,14 +32,22 @@ input:
         type: file
         description: BAM/CRAM/SAM file
         pattern: "*.{bam,cram,sam}"
+        ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+            - edam: "http://edamontology.org/format_3462" # CRAM
+            - edam: "http://edamontology.org/format_2573" # SAM
   - - fasta:
         type: file
         description: OPTIONAL FASTA reference file
         pattern: "*.{fasta,fna,fa}"
+        ontologies:
+            - edam: "http://edamontology.org/format_1332" # FASTA
   - - fai:
         type: file
         description: OPTIONAL FASTA index file from samtools faidx
         pattern: "*.{fai}"
+        ontologies:
+            - edam: "http://edamontology.org/format_1332" # Tabix
   - - specieslist:
         type: file
         description: OPTIONAL text file with list of target reference headers
diff --git a/modules/nf-core/damageprofiler/tests/main.nf.test b/modules/nf-core/damageprofiler/tests/main.nf.test
new file mode 100644
index 000000000000..052e5c8fd669
--- /dev/null
+++ b/modules/nf-core/damageprofiler/tests/main.nf.test
@@ -0,0 +1,130 @@
+nextflow_process {
+
+    name "Test Process DAMAGEPROFILER"
+
+    script "../main.nf"
+    process "DAMAGEPROFILER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "damageprofiler"
+
+    test("homo_sapiens - bam") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'test', single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam',checkIfExists:true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.results.collect { meta, dir -> [
+                        meta, file(dir).list().sort().collect { // Do not check md5sum for .pdf .svg and .log as unstable
+                            file ->
+                            file.endsWith(".pdf") || file.endsWith(".svg") || file.endsWith(".log") ? file : path(dir).resolve(file)
+                        }
+                    ]}
+                ).match() }
+            )
+        }
+    }
+    test("homo_sapiens - bam - fasta fai") {
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists:true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta',checkIfExists:true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai',checkIfExists:true)
+                input[3] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.results.collect { meta, dir -> [
+                        meta, file(dir).list().sort().collect { // Do not check md5sum for .pdf .svg and .log as unstable
+                            file ->
+                            file.endsWith(".pdf") || file.endsWith(".svg") || file.endsWith(".log") ? file : path(dir).resolve(file)
+                        }
+                    ]}
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - bam - header") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'test', single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists:true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.header', checkIfExists:true)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.results.collect { meta, dir -> [
+                        meta, file(dir).listFiles().findAll { it.isDirectory() }.collect { subdir ->
+                            subdir.listFiles().sort().collect { file ->
+                                file.name.endsWith(".pdf") || file.name.endsWith(".svg") || file.name.endsWith(".log") ? file.name : file
+                            }
+                        }.flatten()
+                    ]}
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - bam -- stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'test', single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists:true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/damageprofiler/tests/main.nf.test.snap b/modules/nf-core/damageprofiler/tests/main.nf.test.snap
new file mode 100644
index 000000000000..f1546f6f101b
--- /dev/null
+++ b/modules/nf-core/damageprofiler/tests/main.nf.test.snap
@@ -0,0 +1,204 @@
+{
+    "homo_sapiens - bam - fasta fai": {
+        "content": [
+            [
+                "versions.yml:md5,1822b800e5f67b95cb28901683e9466a"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "3pGtoA_freq.txt:md5,56c165bbc9197e0b3d5bd3d464f9e235",
+                        "3p_freq_misincorporations.txt:md5,62e60259dd7fa2b54cdab6afc1adc9c4",
+                        "5pCtoT_freq.txt:md5,38b5d7c87ec2d8422bc5587095711c5f",
+                        "5p_freq_misincorporations.txt:md5,05e041ff47e7c6d08ede51f5c81a2464",
+                        "DNA_comp_genome.txt:md5,e4d949c6aceddc2c2ef14de9c4aafde5",
+                        "DNA_composition_sample.txt:md5,16be9c91a06fa7defee376230b12862f",
+                        "DamagePlot.pdf",
+                        "DamagePlot_five_prime.svg",
+                        "DamagePlot_three_prime.svg",
+                        "DamageProfiler.log",
+                        "Length_plot.pdf",
+                        "Length_plot_combined_data.svg",
+                        "Length_plot_forward_reverse_separated.svg",
+                        "dmgprof.json:md5,a011a47edaadb3a07527c329a6492570",
+                        "editDistance.txt:md5,7590dac007633ee11025cc99ec9f009b",
+                        "edit_distance.pdf",
+                        "edit_distance.svg",
+                        "lgdistribution.txt:md5,583fd98094de3fb462b133daeaadcf52",
+                        "misincorporation.txt:md5,25119c0fcc8839fdbb3ed10922fb07f4"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T19:15:42.02368625"
+    },
+    "homo_sapiens - bam - header": {
+        "content": [
+            [
+                "versions.yml:md5,1822b800e5f67b95cb28901683e9466a"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "3pGtoA_freq.txt:md5,56c165bbc9197e0b3d5bd3d464f9e235",
+                        "3p_freq_misincorporations.txt:md5,62e60259dd7fa2b54cdab6afc1adc9c4",
+                        "5pCtoT_freq.txt:md5,38b5d7c87ec2d8422bc5587095711c5f",
+                        "5p_freq_misincorporations.txt:md5,05e041ff47e7c6d08ede51f5c81a2464",
+                        "DNA_comp_genome.txt:md5,e4d949c6aceddc2c2ef14de9c4aafde5",
+                        "DNA_composition_sample.txt:md5,16be9c91a06fa7defee376230b12862f",
+                        "DamagePlot.pdf",
+                        "DamagePlot_five_prime.svg",
+                        "DamagePlot_three_prime.svg",
+                        "Length_plot.pdf",
+                        "Length_plot_combined_data.svg",
+                        "Length_plot_forward_reverse_separated.svg",
+                        "dmgprof.json:md5,a011a47edaadb3a07527c329a6492570",
+                        "editDistance.txt:md5,7590dac007633ee11025cc99ec9f009b",
+                        "edit_distance.pdf",
+                        "edit_distance.svg",
+                        "lgdistribution.txt:md5,583fd98094de3fb462b133daeaadcf52",
+                        "misincorporation.txt:md5,25119c0fcc8839fdbb3ed10922fb07f4"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T19:16:12.141583749"
+    },
+    "homo_sapiens - bam": {
+        "content": [
+            [
+                "versions.yml:md5,1822b800e5f67b95cb28901683e9466a"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "3pGtoA_freq.txt:md5,56c165bbc9197e0b3d5bd3d464f9e235",
+                        "3p_freq_misincorporations.txt:md5,62e60259dd7fa2b54cdab6afc1adc9c4",
+                        "5pCtoT_freq.txt:md5,38b5d7c87ec2d8422bc5587095711c5f",
+                        "5p_freq_misincorporations.txt:md5,05e041ff47e7c6d08ede51f5c81a2464",
+                        "DNA_comp_genome.txt:md5,e4d949c6aceddc2c2ef14de9c4aafde5",
+                        "DNA_composition_sample.txt:md5,16be9c91a06fa7defee376230b12862f",
+                        "DamagePlot.pdf",
+                        "DamagePlot_five_prime.svg",
+                        "DamagePlot_three_prime.svg",
+                        "DamageProfiler.log",
+                        "Length_plot.pdf",
+                        "Length_plot_combined_data.svg",
+                        "Length_plot_forward_reverse_separated.svg",
+                        "dmgprof.json:md5,a011a47edaadb3a07527c329a6492570",
+                        "editDistance.txt:md5,7590dac007633ee11025cc99ec9f009b",
+                        "edit_distance.pdf",
+                        "edit_distance.svg",
+                        "lgdistribution.txt:md5,583fd98094de3fb462b133daeaadcf52",
+                        "misincorporation.txt:md5,25119c0fcc8839fdbb3ed10922fb07f4"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T19:15:14.22793253"
+    },
+    "homo_sapiens - bam -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "3pGtoA_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "3p_freq_misincorporations.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "5pCtoT_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "5p_freq_misincorporations.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DNA_comp_genome.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DNA_composition_sample.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamagePlot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamagePlot_five_prime.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamagePlot_three_prime.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamageProfiler.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Length_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Length_plot_combined_data.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Length_plot_forward_reverse_separated.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "dmgprof.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "editDistance.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "edit_distance.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "edit_distance.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "lgdistribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "misincorporation.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1822b800e5f67b95cb28901683e9466a"
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "3pGtoA_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "3p_freq_misincorporations.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "5pCtoT_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "5p_freq_misincorporations.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DNA_comp_genome.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DNA_composition_sample.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamagePlot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamagePlot_five_prime.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamagePlot_three_prime.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "DamageProfiler.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Length_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Length_plot_combined_data.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Length_plot_forward_reverse_separated.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "dmgprof.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "editDistance.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "edit_distance.pdf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "edit_distance.svg:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "lgdistribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "misincorporation.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1822b800e5f67b95cb28901683e9466a"
+                ]
+            },
+            {
+                "DAMAGEPROFILER": {
+                    "damageprofiler": 1.1
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T17:23:23.972121111"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/deseq2/differential/tests/main.nf.test b/modules/nf-core/deseq2/differential/tests/main.nf.test
index 370f05dcd747..b8a63843f13a 100644
--- a/modules/nf-core/deseq2/differential/tests/main.nf.test
+++ b/modules/nf-core/deseq2/differential/tests/main.nf.test
@@ -12,7 +12,7 @@ nextflow_process {
     test("mouse - contrasts - matrix") {
 
         config './contrasts_matrix.config'
-        
+
         when {
             process {
                 """
@@ -24,13 +24,13 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [[],[]]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -52,7 +52,7 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
@@ -72,15 +72,15 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_lengths = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.spoofed_lengths.tsv', checkIfExists: true)
                 ]
-                
+
                 ch_spikes = [[],[]]
 
                 input[0] = ch_contrasts
@@ -105,7 +105,7 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
 
@@ -114,7 +114,7 @@ nextflow_process {
     test("mouse - contrasts - matrix - no blocking") {
 
         config './contrasts_matrix_noblocking.config'
-        
+
         when {
             process {
                 """
@@ -126,13 +126,13 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [[],[]]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -154,7 +154,7 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
@@ -162,7 +162,7 @@ nextflow_process {
     test("mouse - contrasts - matrix - spikes") {
 
         config './contrasts_matrix_spikes.config'
- 
+
         when {
             process {
                 """
@@ -174,16 +174,16 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [
-                    ['id':'ERCC'], 
+                    ['id':'ERCC'],
                     file(expression_test_data_dir + 'SRP254919.spikes.tsv', checkIfExists: true)
                 ]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -205,15 +205,15 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
-    
+
     test("mouse - contrasts - matrix - strip spikes") {
 
         config './contrasts_matrix.config'
- 
+
         when {
             process {
                 """
@@ -225,16 +225,16 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [
-                    ['id':'ERCC'], 
+                    ['id':'ERCC'],
                     file(expression_test_data_dir + 'SRP254919.spikes.tsv', checkIfExists: true)
                 ]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -256,15 +256,15 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
-    
+
     test("mouse - contrasts - matrix - csv") {
 
         config './contrasts_matrix.config'
-        
+
         when {
             process {
                 """
@@ -288,7 +288,7 @@ nextflow_process {
                 }
                 ch_spikes = [[],[]]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -310,15 +310,15 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
-    
+
     test("mouse - contrasts - matrix - vst nsub") {
 
         config './contrasts_matrix_vst_nsub.config'
-        
+
         when {
             process {
                 """
@@ -330,13 +330,13 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [[],[]]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -358,15 +358,15 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
-    
+
     test("mouse - contrasts - matrix - subset to contrast") {
 
         config './contrasts_matrix_subset_to_contrast.config'
-        
+
         when {
             process {
                 """
@@ -378,13 +378,13 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [[],[]]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -406,7 +406,7 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
@@ -414,7 +414,7 @@ nextflow_process {
     test("mouse - contrasts - matrix - exclude samples") {
 
         config './contrasts_matrix_exclude_samples.config'
-        
+
         when {
             process {
                 """
@@ -426,13 +426,13 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [[],[]]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
@@ -454,16 +454,16 @@ nextflow_process {
                     file(process.out.dispersion_plot[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
-                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }                
+                { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
             )
         }
     }
     test("mouse - contrasts - matrix - stub") {
 
         config './contrasts_matrix.config'
-        
+
         options "-stub"
-        
+
         when {
             process {
                 """
@@ -475,13 +475,13 @@ nextflow_process {
                         tuple(it, it.variable, it.reference, it.target)
                     }
                 ch_matrix = [
-                    [id: 'test'], 
+                    [id: 'test'],
                     file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
                     file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 ch_spikes = [[],[]]
                 ch_lengths = [[],[]]
-                
+
                 input[0] = ch_contrasts
                 input[1] = ch_matrix
                 input[2] = ch_spikes
diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml
index bfd8bfb72a8d..198f3fa726df 100644
--- a/modules/nf-core/dragmap/align/environment.yml
+++ b/modules/nf-core/dragmap/align/environment.yml
@@ -3,8 +3,8 @@
 channels:
   - conda-forge
   - bioconda
-
 dependencies:
-  - dragmap=1.3.0
-  - pigz=2.8
-  - samtools=1.18
+  # WARN: Do not update this tool to 1.3.0 until https://github.com/Illumina/DRAGMAP/issues/47 is resolved
+  - bioconda::dragmap=1.2.1
+  - bioconda::samtools=1.19.2
+  - conda-forge::pigz=2.3.4
diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf
index 760c2dfbad0a..3f6ea7536605 100644
--- a/modules/nf-core/dragmap/align/main.nf
+++ b/modules/nf-core/dragmap/align/main.nf
@@ -1,26 +1,27 @@
 process DRAGMAP_ALIGN {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:7eed251370ac7f3537c3d9472cdb2f9f5d8da1c5-0':
-        'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:7eed251370ac7f3537c3d9472cdb2f9f5d8da1c5-0' }"
+    // WARN: Do not update this tool to 1.3.0 until https://github.com/Illumina/DRAGMAP/issues/47 is resolved
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:df80ed8d23d0a2c43181a2b3dd1b39f2d00fab5c-0'
+        : 'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:df80ed8d23d0a2c43181a2b3dd1b39f2d00fab5c-0'}"
 
     input:
-    tuple val(meta) , path(reads)
+    tuple val(meta), path(reads)
     tuple val(meta2), path(hashmap)
     tuple val(meta3), path(fasta)
-    val   sort_bam
+    val sort_bam
 
     output:
-    tuple val(meta), path("*.sam")  , emit: sam   , optional: true
-    tuple val(meta), path("*.bam")  , emit: bam   , optional: true
-    tuple val(meta), path("*.cram") , emit: cram  , optional: true
-    tuple val(meta), path("*.crai") , emit: crai  , optional: true
-    tuple val(meta), path("*.csi")  , emit: csi   , optional: true
-    tuple val(meta), path('*.log')  , emit: log
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.sam"),  emit: sam,  optional: true
+    tuple val(meta), path("*.bam"),  emit: bam,  optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.crai"), emit: crai, optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,  optional: true
+    tuple val(meta), path('*.log'),  emit: log
+    path "versions.yml",             emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,22 +30,24 @@ process DRAGMAP_ALIGN {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reads_command       = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
-    def samtools_command    = sort_bam ? 'sort' : 'view'
-    def extension_pattern   = /(--output-fmt|-O)+\s+(\S+)/
-    def extension_matcher   =  (args2 =~ extension_pattern)
-    def extension           = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    def reference           = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+    def reads_command = meta.single_end ? "-1 ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
+    def samtools_command = sort_bam ? 'sort' : 'view'
+    def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
+    def extension_matcher = (args2 =~ extension_pattern)
+    def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
+    def reference = fasta && extension == "cram" ? "--reference ${fasta}" : ""
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
 
     """
     dragen-os \\
-        -r $hashmap \\
-        $args \\
-        --num-threads $task.cpus \\
-        $reads_command \\
+        -r ${hashmap} \\
+        ${args} \\
+        --num-threads ${task.cpus} \\
+        ${reads_command} \\
         2> >(tee ${prefix}.dragmap.log >&2) \\
-        | samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -
+        | samtools ${samtools_command} ${args2} --threads ${task.cpus} ${reference} -o ${prefix}.${extension} -
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -58,14 +61,17 @@ process DRAGMAP_ALIGN {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
-    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension_matcher = (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
 
     def create_index = ""
     if (extension == "cram") {
         create_index = "touch ${prefix}.crai"
-    } else if (extension == "bam") {
+    }
+    else if (extension == "bam") {
         create_index = "touch ${prefix}.csi"
     }
 
diff --git a/modules/nf-core/dragmap/align/tests/main.nf.test b/modules/nf-core/dragmap/align/tests/main.nf.test
index d688c291c137..5abe76f6a757 100644
--- a/modules/nf-core/dragmap/align/tests/main.nf.test
+++ b/modules/nf-core/dragmap/align/tests/main.nf.test
@@ -40,12 +40,13 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll (
-                { assert process.success },
                 { assert snapshot(
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
                 ).match() }
             )
         }
@@ -83,12 +84,13 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll (
-                { assert process.success },
                 { assert snapshot(
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
                 ).match() }
             )
         }
@@ -129,12 +131,13 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll (
-                { assert process.success },
                 { assert snapshot(
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
                 ).match() }
             )
         }
@@ -175,12 +178,13 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll (
-                { assert process.success },
                 { assert snapshot(
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
                 ).match() }
             )
         }
@@ -221,12 +225,13 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll (
-                { assert process.success },
                 { assert snapshot(
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
                 ).match() }
             )
         }
@@ -268,16 +273,13 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll (
-                { assert process.success },
                 { assert snapshot(
-                    file(process.out.bam[0][1]).name,
-                    file(process.out.log[0][1]).name,
-                    file(process.out.versions[0]).name
+                    process.out,
+                    path(process.out.versions[0]).yaml
                 ).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/dragmap/align/tests/main.nf.test.snap b/modules/nf-core/dragmap/align/tests/main.nf.test.snap
index 4bd60ebf49d5..9a63fde0071f 100644
--- a/modules/nf-core/dragmap/align/tests/main.nf.test.snap
+++ b/modules/nf-core/dragmap/align/tests/main.nf.test.snap
@@ -10,13 +10,22 @@
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
             ],
-            "versions.yml"
+            [
+                "versions.yml:md5,bec50713b6dac1cc16fe68b731848394"
+            ],
+            {
+                "DRAGMAP_ALIGN": {
+                    "dragmap": "1.2.1",
+                    "samtools": "1.19.2",
+                    "pigz": "2.3.4"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-03-20T10:46:54.961203552"
+        "timestamp": "2025-04-10T11:33:50.428894432"
     },
     "homo_sapiens - [fastq1, fastq2], hashtable, fasta, true": {
         "content": [
@@ -29,13 +38,22 @@
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
             ],
-            "versions.yml"
+            [
+                "versions.yml:md5,bec50713b6dac1cc16fe68b731848394"
+            ],
+            {
+                "DRAGMAP_ALIGN": {
+                    "dragmap": "1.2.1",
+                    "samtools": "1.19.2",
+                    "pigz": "2.3.4"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-03-20T10:47:24.495131137"
+        "timestamp": "2025-04-10T11:34:27.492548556"
     },
     "sarscov2 - fastq, hashtable, fasta, true": {
         "content": [
@@ -48,13 +66,22 @@
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
             ],
-            "versions.yml"
+            [
+                "versions.yml:md5,bec50713b6dac1cc16fe68b731848394"
+            ],
+            {
+                "DRAGMAP_ALIGN": {
+                    "dragmap": "1.2.1",
+                    "samtools": "1.19.2",
+                    "pigz": "2.3.4"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-03-20T10:46:42.57679755"
+        "timestamp": "2025-04-10T11:33:39.843877739"
     },
     "sarscov2 - [fastq1, fastq2], hashtable, fasta, true": {
         "content": [
@@ -67,25 +94,118 @@
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
             ],
-            "versions.yml"
+            [
+                "versions.yml:md5,bec50713b6dac1cc16fe68b731848394"
+            ],
+            {
+                "DRAGMAP_ALIGN": {
+                    "dragmap": "1.2.1",
+                    "samtools": "1.19.2",
+                    "pigz": "2.3.4"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-03-20T10:47:08.943445149"
+        "timestamp": "2025-04-10T11:34:00.702498161"
     },
     "sarscov2 - [fastq1, fastq2], hashtable, fasta, true - stub": {
         "content": [
-            "test.bam",
-            "test.log",
-            "versions.yml"
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,bec50713b6dac1cc16fe68b731848394"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sam": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,bec50713b6dac1cc16fe68b731848394"
+                ]
+            },
+            {
+                "DRAGMAP_ALIGN": {
+                    "dragmap": "1.2.1",
+                    "samtools": "1.19.2",
+                    "pigz": "2.3.4"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-03-20T10:47:38.346392133"
+        "timestamp": "2025-04-10T11:13:17.187912755"
     },
     "sarscov2 - fastq, hashtable, fasta, false": {
         "content": [
@@ -98,12 +218,21 @@
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
             ],
-            "versions.yml"
+            [
+                "versions.yml:md5,bec50713b6dac1cc16fe68b731848394"
+            ],
+            {
+                "DRAGMAP_ALIGN": {
+                    "dragmap": "1.2.1",
+                    "samtools": "1.19.2",
+                    "pigz": "2.3.4"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-03-20T10:46:28.406548681"
+        "timestamp": "2025-04-10T11:33:28.056988229"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/dragmap/hashtable/environment.yml b/modules/nf-core/dragmap/hashtable/environment.yml
index abd4d3f261e3..8225f820ca51 100644
--- a/modules/nf-core/dragmap/hashtable/environment.yml
+++ b/modules/nf-core/dragmap/hashtable/environment.yml
@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::dragmap=1.3.0
+  # WARN: Do not update this tool to 1.3.0 until https://github.com/Illumina/DRAGMAP/issues/47 is resolved
+  - bioconda::dragmap=1.2.1
diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf
index 24792d7b9c65..e86b110094a8 100644
--- a/modules/nf-core/dragmap/hashtable/main.nf
+++ b/modules/nf-core/dragmap/hashtable/main.nf
@@ -1,18 +1,19 @@
 process DRAGMAP_HASHTABLE {
-    tag "$fasta"
+    tag "${fasta}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dragmap:1.3.0--h91baf5a_3':
-        'biocontainers/dragmap:1.3.0--h91baf5a_3' }"
+    // WARN: Do not update this tool to 1.3.0 until https://github.com/Illumina/DRAGMAP/issues/47 is resolved
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--h72d16da_1'
+        : 'biocontainers/dragmap:1.2.1--h72d16da_1'}"
 
     input:
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path("dragmap")    , emit: hashmap
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("dragmap"), emit: hashmap
+    path "versions.yml",              emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,10 +24,10 @@ process DRAGMAP_HASHTABLE {
     mkdir dragmap
     dragen-os \\
         --build-hash-table true \\
-        --ht-reference $fasta \\
+        --ht-reference ${fasta} \\
         --output-directory dragmap \\
-        $args \\
-        --ht-num-threads $task.cpus
+        ${args} \\
+        --ht-num-threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -43,5 +44,4 @@ process DRAGMAP_HASHTABLE {
         dragmap: \$(echo \$(dragen-os --version 2>&1))
     END_VERSIONS
     """
-
 }
diff --git a/modules/nf-core/dragmap/hashtable/tests/main.nf.test b/modules/nf-core/dragmap/hashtable/tests/main.nf.test
index 474039911f4f..f22b453feb4d 100644
--- a/modules/nf-core/dragmap/hashtable/tests/main.nf.test
+++ b/modules/nf-core/dragmap/hashtable/tests/main.nf.test
@@ -23,16 +23,16 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll(
-                { assert process.success },
                 { assert snapshot(
                         file(process.out.hashmap[0][1]).name,
-                        file(process.out.versions[0]).name
+                        process.out.versions,
+                        path(process.out.versions[0]).yaml
                     ).match()
                 }
             )
         }
-
     }
 
     test("sarscov2 - fasta - stub") {
@@ -51,19 +51,16 @@ nextflow_process {
         }
 
         then {
+            assert { process.success }
             assertAll(
-                { assert process.success },
                 { assert snapshot(
-                        file(process.out.hashmap[0][1]).name,
-                        file(process.out.versions[0]).name
-                    ).match()
-                }
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
     // TODO Add test using alt-masked bed file
     // https://github.com/Illumina/dragmap#build-hash-table-using-an-alt-masked-bed-file
-
 }
diff --git a/modules/nf-core/dragmap/hashtable/tests/main.nf.test.snap b/modules/nf-core/dragmap/hashtable/tests/main.nf.test.snap
index 9b4b90d8a3cb..af7efb419b0e 100644
--- a/modules/nf-core/dragmap/hashtable/tests/main.nf.test.snap
+++ b/modules/nf-core/dragmap/hashtable/tests/main.nf.test.snap
@@ -1,16 +1,62 @@
 {
     "sarscov2 - fasta - stub": {
         "content": [
-            "dragmap",
-            "versions.yml"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,050c28333b92fac50eec250c28b841d0"
+                ],
+                "hashmap": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,050c28333b92fac50eec250c28b841d0"
+                ]
+            },
+            {
+                "DRAGMAP_HASHTABLE": {
+                    "dragmap": "1.2.1"
+                }
+            }
         ],
-        "timestamp": "2023-11-22T13:42:22.53412378"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-10T11:34:52.49644133"
     },
     "sarscov2 - fasta": {
         "content": [
             "dragmap",
-            "versions.yml"
+            [
+                "versions.yml:md5,050c28333b92fac50eec250c28b841d0"
+            ],
+            {
+                "DRAGMAP_HASHTABLE": {
+                    "dragmap": "1.2.1"
+                }
+            }
         ],
-        "timestamp": "2023-11-22T12:53:25.493202451"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-10T11:34:44.786652653"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
index cac59e882060..ca3c7434b74d 100644
--- a/modules/nf-core/ensemblvep/download/environment.yml
+++ b/modules/nf-core/ensemblvep/download/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ensembl-vep=113.0
+  - bioconda::ensembl-vep=113.4
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
index 0664a2dfb929..bed8c858b421 100644
--- a/modules/nf-core/ensemblvep/download/main.nf
+++ b/modules/nf-core/ensemblvep/download/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_DOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' :
-        'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
+        'https://depot.galaxyproject.org/singularity/ensembl-vep:113.4--pl5321h2a3209d_0' :
+        'biocontainers/ensembl-vep:113.4--pl5321h2a3209d_0' }"
 
     input:
     tuple val(meta), val(assembly), val(species), val(cache_version)
diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml
index cac59e882060..ca3c7434b74d 100644
--- a/modules/nf-core/ensemblvep/filtervep/environment.yml
+++ b/modules/nf-core/ensemblvep/filtervep/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ensembl-vep=113.0
+  - bioconda::ensembl-vep=113.4
diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf
index 69245df0e27c..94a1b7104ff9 100644
--- a/modules/nf-core/ensemblvep/filtervep/main.nf
+++ b/modules/nf-core/ensemblvep/filtervep/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_FILTERVEP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' :
-        'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
+        'https://depot.galaxyproject.org/singularity/ensembl-vep:113.4--pl5321h2a3209d_0' :
+        'biocontainers/ensembl-vep:113.4--pl5321h2a3209d_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
index cac59e882060..ca3c7434b74d 100644
--- a/modules/nf-core/ensemblvep/vep/environment.yml
+++ b/modules/nf-core/ensemblvep/vep/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ensembl-vep=113.0
+  - bioconda::ensembl-vep=113.4
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
index 7bd74fc4ae32..b57c236d0442 100644
--- a/modules/nf-core/ensemblvep/vep/main.nf
+++ b/modules/nf-core/ensemblvep/vep/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' :
-        'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
+        'https://depot.galaxyproject.org/singularity/ensembl-vep:113.4--pl5321h2a3209d_0' :
+        'biocontainers/ensembl-vep:113.4--pl5321h2a3209d_0' }"
 
     input:
     tuple val(meta), path(vcf), path(custom_extra_files)
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154a417..23e16634c303 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,7 @@ process FASTQC {
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
     // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fcs/fcsgx/main.nf b/modules/nf-core/fcs/fcsgx/main.nf
index 1244b9b768d8..6e323385955e 100644
--- a/modules/nf-core/fcs/fcsgx/main.nf
+++ b/modules/nf-core/fcs/fcsgx/main.nf
@@ -1,3 +1,10 @@
+def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/modules/fcsgx/rungx
+
+Reason:
+This module is now renamed as FCSGX_RUNGX and as been updated to the latest version
+"""
+
 process FCS_FCSGX {
     tag "$meta.id"
     label 'process_low'
@@ -13,12 +20,15 @@ process FCS_FCSGX {
     output:
     tuple val(meta), path("out/*.fcs_gx_report.txt"), emit: fcs_gx_report
     tuple val(meta), path("out/*.taxonomy.rpt")     , emit: taxonomy_report
-    path "versions.yml"                         , emit: versions
+    path "versions.yml"                             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    // Comment out this block to disable the deprecation warning
+    assert false: deprecation_message
+
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "FCS_FCSGX module does not support Conda. Please use Docker / Singularity / Podman instead."
@@ -43,6 +53,9 @@ process FCS_FCSGX {
     """
 
     stub:
+    // Comment out this block to disable the deprecation warning
+    assert false: deprecation_message
+
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "FCS_FCSGX module does not support Conda. Please use Docker / Singularity / Podman instead."
diff --git a/modules/nf-core/fcs/fcsgx/tests/main.nf.test b/modules/nf-core/fcs/fcsgx/tests/main.nf.test
new file mode 100644
index 000000000000..61a547122812
--- /dev/null
+++ b/modules/nf-core/fcs/fcsgx/tests/main.nf.test
@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process FCS_FCSGX"
+    script "../main.nf"
+    process "FCS_FCSGX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fcs"
+    tag "fcs/fcsgx"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.errorReport.contains("WARNING: This module has been deprecated. Please use nf-core/modules/fcsgx/rungx")}
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.errorReport.contains("WARNING: This module has been deprecated. Please use nf-core/modules/fcsgx/rungx")}
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/freyja/boot/environment.yml b/modules/nf-core/freyja/boot/environment.yml
index 0b5b6b06f37c..2211302befe6 100644
--- a/modules/nf-core/freyja/boot/environment.yml
+++ b/modules/nf-core/freyja/boot/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::freyja=1.5.0
+  - bioconda::freyja=1.5.3
diff --git a/modules/nf-core/freyja/boot/main.nf b/modules/nf-core/freyja/boot/main.nf
index ca1f1a3515a7..253848d2ea47 100644
--- a/modules/nf-core/freyja/boot/main.nf
+++ b/modules/nf-core/freyja/boot/main.nf
@@ -5,8 +5,8 @@ process FREYJA_BOOT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
-        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.3--pyhdfd78af_1' :
+        'biocontainers/freyja:1.5.3--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(variants), path(depths)
diff --git a/modules/nf-core/freyja/boot/tests/main.nf.test.snap b/modules/nf-core/freyja/boot/tests/main.nf.test.snap
index 334c743f2d57..7ab54236eff6 100644
--- a/modules/nf-core/freyja/boot/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/boot/tests/main.nf.test.snap
@@ -2,13 +2,13 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,a2af061943f186aa529b80a419a8fcc1"
+                "versions.yml:md5,89cd12da2e4e4c6de66bf39a5eb3ec57"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-02T16:10:15.064948172"
+        "timestamp": "2025-04-01T16:54:39.243225144"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/freyja/demix/environment.yml b/modules/nf-core/freyja/demix/environment.yml
index 0b5b6b06f37c..2211302befe6 100644
--- a/modules/nf-core/freyja/demix/environment.yml
+++ b/modules/nf-core/freyja/demix/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::freyja=1.5.0
+  - bioconda::freyja=1.5.3
diff --git a/modules/nf-core/freyja/demix/main.nf b/modules/nf-core/freyja/demix/main.nf
index 0ae3246bafb8..713fcab392e9 100644
--- a/modules/nf-core/freyja/demix/main.nf
+++ b/modules/nf-core/freyja/demix/main.nf
@@ -5,8 +5,8 @@ process FREYJA_DEMIX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
-        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.3--pyhdfd78af_1' :
+        'biocontainers/freyja:1.5.3--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(variants), path(depths)
diff --git a/modules/nf-core/freyja/demix/tests/main.nf.test.snap b/modules/nf-core/freyja/demix/tests/main.nf.test.snap
index f36e9cc6c80d..27b02fbb4447 100644
--- a/modules/nf-core/freyja/demix/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/demix/tests/main.nf.test.snap
@@ -2,13 +2,13 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,a9c5d4ae8f93de8cbc08c7d87debd89c"
+                "versions.yml:md5,5076e7980c56cec60dc362b60bc2fd2e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-02T16:10:46.778891705"
+        "timestamp": "2025-03-28T13:58:06.868765486"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/freyja/update/environment.yml b/modules/nf-core/freyja/update/environment.yml
index 0b5b6b06f37c..a5625a29f45b 100644
--- a/modules/nf-core/freyja/update/environment.yml
+++ b/modules/nf-core/freyja/update/environment.yml
@@ -1,7 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
-  - conda-forge
   - bioconda
+  - conda-forge
 dependencies:
-  - bioconda::freyja=1.5.0
+  - bioconda::freyja=1.5.3
diff --git a/modules/nf-core/freyja/update/main.nf b/modules/nf-core/freyja/update/main.nf
index 4d4b6857c60f..36311b170fca 100644
--- a/modules/nf-core/freyja/update/main.nf
+++ b/modules/nf-core/freyja/update/main.nf
@@ -5,14 +5,14 @@ process FREYJA_UPDATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
-        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.3--pyhdfd78af_1' :
+        'biocontainers/freyja:1.5.3--pyhdfd78af_1' }"
 
     input:
     val db_name
 
     output:
-    path "${db_name}/usher_barcodes.csv"   , emit: barcodes
+    path "${db_name}/usher_barcodes.feather"   , emit: barcodes
     path "${db_name}/lineages.yml"         , emit: lineages_topology
     path "${db_name}/curated_lineages.json", emit: lineages_meta
     path "versions.yml"                    , emit: versions
diff --git a/modules/nf-core/freyja/update/meta.yml b/modules/nf-core/freyja/update/meta.yml
index a61b0676f2c3..e962aa5ec8d5 100644
--- a/modules/nf-core/freyja/update/meta.yml
+++ b/modules/nf-core/freyja/update/meta.yml
@@ -20,10 +20,10 @@ input:
         description: "The name of the database directory"
 output:
   - barcodes:
-      - ${db_name}/usher_barcodes.csv:
+      - ${db_name}/usher_barcodes.feather:
           type: file
           description: File containing lineage defining barcodes
-          pattern: "*barcodes.csv"
+          pattern: "*barcodes.feather"
   - lineages_topology:
       - ${db_name}/lineages.yml:
           type: file
diff --git a/modules/nf-core/freyja/update/tests/main.nf.test.snap b/modules/nf-core/freyja/update/tests/main.nf.test.snap
index 0f510c6236b5..2d8b91e10daf 100644
--- a/modules/nf-core/freyja/update/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/update/tests/main.nf.test.snap
@@ -2,13 +2,13 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,c730cb8a7d262beaace190a3e832a54d"
+                "versions.yml:md5,6caaebe148beed288dfd00f2af1eaccc"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-02T16:11:08.501478371"
+        "timestamp": "2025-03-28T12:16:49.598775067"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/freyja/variants/environment.yml b/modules/nf-core/freyja/variants/environment.yml
index 0b5b6b06f37c..a5625a29f45b 100644
--- a/modules/nf-core/freyja/variants/environment.yml
+++ b/modules/nf-core/freyja/variants/environment.yml
@@ -1,7 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
-  - conda-forge
   - bioconda
+  - conda-forge
 dependencies:
-  - bioconda::freyja=1.5.0
+  - bioconda::freyja=1.5.3
diff --git a/modules/nf-core/freyja/variants/main.nf b/modules/nf-core/freyja/variants/main.nf
index fc8769712a04..2f7e4020b077 100644
--- a/modules/nf-core/freyja/variants/main.nf
+++ b/modules/nf-core/freyja/variants/main.nf
@@ -5,8 +5,8 @@ process FREYJA_VARIANTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
-        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.3--pyhdfd78af_1' :
+        'biocontainers/freyja:1.5.3--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/freyja/variants/tests/main.nf.test.snap b/modules/nf-core/freyja/variants/tests/main.nf.test.snap
index c85e803266b3..607eea84704a 100644
--- a/modules/nf-core/freyja/variants/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/variants/tests/main.nf.test.snap
@@ -13,7 +13,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,10000e2412ba93678d3a4345fd98a2e3"
+                    "versions.yml:md5,44e6cfa152c1ba5dd5c424c804a0c062"
                 ],
                 "variants": [
                     [
@@ -26,14 +26,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,10000e2412ba93678d3a4345fd98a2e3"
+                    "versions.yml:md5,44e6cfa152c1ba5dd5c424c804a0c062"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-02T16:11:32.315489497"
+        "timestamp": "2025-03-28T12:42:58.200885929"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fusioncatcher/build/environment.yml b/modules/nf-core/fusioncatcher/build/environment.yml
new file mode 100644
index 000000000000..25f7417c5ac0
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/build/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fusioncatcher=1.33"
diff --git a/modules/nf-core/fusioncatcher/build/main.nf b/modules/nf-core/fusioncatcher/build/main.nf
new file mode 100644
index 000000000000..c24865abb28f
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/build/main.nf
@@ -0,0 +1,45 @@
+process FUSIONCATCHER_BUILD {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fusioncatcher:1.33--hdfd78af_5':
+        'biocontainers/fusioncatcher:1.33--hdfd78af_5' }"
+
+    input:
+    val(meta)
+
+    output:
+    tuple val(meta), path("${prefix}")  , emit: reference
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    fusioncatcher-build \\
+        ${args} \\
+        --output=${prefix} \\
+        --threads=${task.cpus}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fusioncatcher/build/meta.yml b/modules/nf-core/fusioncatcher/build/meta.yml
new file mode 100644
index 000000000000..54ccb5237ca1
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/build/meta.yml
@@ -0,0 +1,47 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fusioncatcher_build"
+description: Build references for fusioncatcher
+keywords:
+  - references
+  - fusions
+  - rna
+
+tools:
+  - fusioncatcher:
+      description: Build genome for fusioncatcher
+      homepage: https://github.com/ndaniel/fusioncatcher/
+      documentation: https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md
+      tool_dev_url: https://github.com/ndaniel/fusioncatcher/
+      doi: "10.1101/011650"
+      licence: ["GPL v3"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+
+output:
+  - reference:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - ${prefix}:
+        type: file
+        description: Diretory containing the fusioncatcher reference files
+
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/fusioncatcher/build/tests/main.nf.test b/modules/nf-core/fusioncatcher/build/tests/main.nf.test
new file mode 100644
index 000000000000..315c1b117320
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/build/tests/main.nf.test
@@ -0,0 +1,35 @@
+nextflow_process {
+
+    name "Test Process FUSIONCATCHER_BUILD"
+    script "../main.nf"
+    process "FUSIONCATCHER_BUILD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fusioncatcher"
+    tag "fusioncatcher/build"
+
+    // Only stub tests because this module downloads about 50 GB of data
+
+    test("stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ id:'test', single_end:false ] // meta map
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fusioncatcher/build/tests/main.nf.test.snap b/modules/nf-core/fusioncatcher/build/tests/main.nf.test.snap
new file mode 100644
index 000000000000..4a301fcb7993
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/build/tests/main.nf.test.snap
@@ -0,0 +1,41 @@
+{
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e049cf8ceb55a41bd8f05db0931a8c14"
+                ],
+                "reference": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e049cf8ceb55a41bd8f05db0931a8c14"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-10T16:50:59.596294661"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/environment.yml b/modules/nf-core/fusioncatcher/fusioncatcher/environment.yml
new file mode 100644
index 000000000000..25f7417c5ac0
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fusioncatcher=1.33"
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/main.nf b/modules/nf-core/fusioncatcher/fusioncatcher/main.nf
new file mode 100644
index 000000000000..5c2a8f38dd02
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/main.nf
@@ -0,0 +1,65 @@
+process FUSIONCATCHER_FUSIONCATCHER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fusioncatcher:1.33--hdfd78af_5':
+        'biocontainers/fusioncatcher:1.33--hdfd78af_5' }"
+
+    input:
+    tuple val(meta), path(fastqs)
+    tuple val(meta2), path(reference)
+
+    output:
+    tuple val(meta), path("*.fusion-genes.txt"), emit: fusions, optional: true
+    tuple val(meta), path("*.summary.txt")     , emit: summary, optional: true
+    tuple val(meta), path("*.log")             , emit: log
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input = fastqs.join(",")
+
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[FusionCatcher] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    fusioncatcher \\
+        --input=${input} \\
+        --output=. \\
+        --data=${reference} \\
+        --threads=${task.cpus} \\
+        --Xmx=${avail_mem} \\
+        ${args}
+
+    mv final-list_candidate-fusion-genes.txt ${prefix}.fusion-genes.txt
+    mv summary_candidate_fusions.txt ${prefix}.summary.txt
+    mv fusioncatcher.log ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fusion-genes.txt
+    touch ${prefix}.summary.txt
+    touch ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/meta.yml b/modules/nf-core/fusioncatcher/fusioncatcher/meta.yml
new file mode 100644
index 000000000000..bfd7848efd59
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/meta.yml
@@ -0,0 +1,78 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fusioncatcher_fusioncatcher"
+description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
+keywords:
+  - fusion
+  - rna
+  - fastq
+tools:
+  - fusioncatcher:
+      description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
+      homepage: https://github.com/ndaniel/fusioncatcher
+      documentation: https://github.com/ndaniel/fusioncatcher/wiki
+      tool_dev_url: https://github.com/ndaniel/fusioncatcher
+      doi: "10.1101/011650v1"
+      licence: ["GPL v3"]
+      identifier: biotools:fusioncatcher
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fastqs:
+        type: list
+        description: A list of input fastq files
+        pattern: "*.{fastq,fq}.gz"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reference:
+        type: file
+        description: Directory containing fusioncatcher reference files
+
+output:
+  - fusions:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.fusion-genes.txt":
+        type: file
+        description: The detected fusions in the input files
+        pattern: "*.fusion-genes.txt"
+  - summary:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.summary.txt":
+        type: file
+        description: The generated summary
+        pattern: "*.summary.txt"
+  - log:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.log":
+        type: file
+        description: The Fusioncatcher log
+        pattern: "*.log"
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test
new file mode 100644
index 000000000000..28e9d13ecaa4
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test
@@ -0,0 +1,43 @@
+nextflow_process {
+
+    name "Test Process FUSIONCATCHER_FUSIONCATCHER"
+    script "../main.nf"
+    process "FUSIONCATCHER_FUSIONCATCHER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fusioncatcher"
+    tag "fusioncatcher/fusioncatcher"
+
+    // Only stub tests because the refernce is about 50 GB of data
+
+    test("sarscov2 - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'reference'],
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test.snap b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test.snap
new file mode 100644
index 000000000000..a1916e55308a
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test.snap
@@ -0,0 +1,73 @@
+{
+    "sarscov2 - fastq - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fusion-genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,6a54daab2ec7621d8493678e832cf45e"
+                ],
+                "fusions": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fusion-genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6a54daab2ec7621d8493678e832cf45e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T11:01:13.392512529"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/modelsegments/environment.yml b/modules/nf-core/gatk4/modelsegments/environment.yml
new file mode 100644
index 000000000000..b562b72c740c
--- /dev/null
+++ b/modules/nf-core/gatk4/modelsegments/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/modelsegments/main.nf b/modules/nf-core/gatk4/modelsegments/main.nf
new file mode 100644
index 000000000000..c3f229685dee
--- /dev/null
+++ b/modules/nf-core/gatk4/modelsegments/main.nf
@@ -0,0 +1,54 @@
+process GATK4_MODELSEGMENTS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
+
+    input:
+    tuple val(meta), path(counts)
+
+    output:
+    tuple val(meta), path("*.modelFinal.seg"), emit: segmented
+    path "versions.yml"                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[GATK ModelSegments] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+     gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
+       ModelSegments \\
+        ${args} \\
+        --tmp-dir . \\
+        --denoised-copy-ratios ${counts} \\
+        -O ./ \\
+        --output-prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.modelFinal.seg
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gatk4/modelsegments/meta.yml b/modules/nf-core/gatk4/modelsegments/meta.yml
new file mode 100644
index 000000000000..91b35a5fc4cc
--- /dev/null
+++ b/modules/nf-core/gatk4/modelsegments/meta.yml
@@ -0,0 +1,49 @@
+name: "gatk4_modelsegments"
+description: Converts copy number ratios (and optonally allelic counts) to copy number
+  segments
+keywords:
+  - copyratios
+  - modelsegments
+  - gatk4
+tools:
+  - gatk4:
+      description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      doi: 10.1158/1538-7445.AM2017-3590
+      tool_dev_url: "https://github.com/broadinstitute/gatk"
+      licence: ["Apache-2.0"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - counts:
+        type: file
+        description: Denoised copy ratios in hdf5 format.
+        pattern: "*.{hdf5}"
+output:
+  - segmented:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.modelFinal.seg":
+          type: file
+          description: Copy number ratio segments.
+          pattern: "*.{seg}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@lbeltrame"
+maintainers:
+  - "@lbeltrame"
diff --git a/modules/nf-core/gatk4/modelsegments/tests/main.nf.test b/modules/nf-core/gatk4/modelsegments/tests/main.nf.test
new file mode 100644
index 000000000000..ccad77ba72e5
--- /dev/null
+++ b/modules/nf-core/gatk4/modelsegments/tests/main.nf.test
@@ -0,0 +1,120 @@
+nextflow_process {
+
+    name "Test Process GATK4_MODELSEGMENTS"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "GATK4_MODELSEGMENTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/createreadcountpanelofnormals"
+    tag "gatk4/collectreadcounts"
+    tag "gatk4/preprocessintervals"
+    tag "gatk4/denoisereadcounts"
+    tag "gatk4/modelsegments"
+
+    setup {
+        run("GATK4_PREPROCESSINTERVALS"){
+            script "../../preprocessintervals/main.nf"
+
+            process {
+                """
+                input[0] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)])
+                input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)])
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                """
+            }
+        }
+        run("GATK4_COLLECTREADCOUNTS"){
+            script "../../collectreadcounts/main.nf"
+
+            process {
+                """
+                intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map {meta, list -> list}
+                input[0] = Channel.of(
+                    [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)],
+                )
+                .combine( intervals)
+                input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)])
+                input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)])
+                """
+            }
+        }
+        run("GATK4_CREATEREADCOUNTPANELOFNORMALS"){
+            script "../../createreadcountpanelofnormals/main.nf"
+
+            process {
+                """
+                input[0] = GATK4_COLLECTREADCOUNTS.out.tsv.groupTuple()
+                """
+            }
+        }
+
+        run("GATK4_DENOISEREADCOUNTS"){
+            script "../../denoisereadcounts/main.nf"
+            process {
+                """
+                input[0] = GATK4_COLLECTREADCOUNTS.out.tsv.first()
+                input[1] = GATK4_CREATEREADCOUNTPANELOFNORMALS.out.pon
+                """
+            }
+        }
+    }
+
+    test("human - modelsegments") {
+
+        when {
+
+            params {
+                gatk4_collectreadcounts_args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY"
+                gatk4_createreadcountpanelofnormals_args = "--minimum-interval-median-percentile 1.0 --number-of-eigensamples 2"
+            }
+
+            process {
+                """
+                input[0] = GATK4_DENOISEREADCOUNTS.out.denoised.first()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - modelsegments - stub") {
+
+        options "-stub "
+
+        when {
+
+            params {
+                gatk4_collectreadcounts_args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY"
+                gatk4_createreadcountpanelofnormals_args = "--minimum-interval-median-percentile 1.0 --number-of-eigensamples 2"
+            }
+
+            process {
+                """
+                input[0] = GATK4_DENOISEREADCOUNTS.out.denoised.first()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/modelsegments/tests/main.nf.test.snap b/modules/nf-core/gatk4/modelsegments/tests/main.nf.test.snap
new file mode 100644
index 000000000000..c15c37874ff6
--- /dev/null
+++ b/modules/nf-core/gatk4/modelsegments/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "human - modelsegments": {
+        "content": [
+            {
+               "0": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            "test.modelFinal.seg:md5,d4854bf6442d7169c5cf204a3c5e095d"
+                        ]
+               ],
+                "1": [
+                    "versions.yml:md5,fdcfa40d7f7e508c6abb587aea88f033"
+                ],
+               "segmented": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.modelFinal.seg:md5,d4854bf6442d7169c5cf204a3c5e095d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,fdcfa40d7f7e508c6abb587aea88f033"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:33:41.980566137"
+    },
+    "human - modelsegments - stub": {
+        "content": [
+            {
+               "0": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            "test.modelFinal.seg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+               ],
+                "1": [
+                    "versions.yml:md5,fdcfa40d7f7e508c6abb587aea88f033"
+                ],
+               "segmented": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.modelFinal.seg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,fdcfa40d7f7e508c6abb587aea88f033"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:33:41.980566137"
+    }
+}
diff --git a/modules/nf-core/gatk4/modelsegments/tests/nextflow.config b/modules/nf-core/gatk4/modelsegments/tests/nextflow.config
new file mode 100644
index 000000000000..1f7744fb30ee
--- /dev/null
+++ b/modules/nf-core/gatk4/modelsegments/tests/nextflow.config
@@ -0,0 +1,9 @@
+docker.runOptions = '--platform=linux/amd64 -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME'
+process {
+    withName: GATK4_COLLECTREADCOUNTS {
+        ext.args = params.gatk4_collectreadcounts_args
+    }
+    withName: GATK4_CREATEREADCOUNTPANELOFNORMALS {
+        ext.args = params.gatk4_createreadcountpanelofnormals_args
+    }
+}
diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf
index 3ac374e03564..756dfca9429e 100644
--- a/modules/nf-core/gatk4/mutect2/main.nf
+++ b/modules/nf-core/gatk4/mutect2/main.nf
@@ -62,10 +62,10 @@ process GATK4_MUTECT2 {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
     touch ${prefix}.vcf.gz.stats
-    touch ${prefix}.f1r2.tar.gz
+    echo "" | gzip > ${prefix}.f1r2.tar.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/gatk4/mutect2/tests/f1r2.config b/modules/nf-core/gatk4/mutect2/tests/f1r2.config
deleted file mode 100644
index 2d3c8a1708a0..000000000000
--- a/modules/nf-core/gatk4/mutect2/tests/f1r2.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
-    ext.args = { "--normal-sample $meta.normal_id --f1r2-tar-gz ${meta.id}.f1r2.tar.gz" }
-}
diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test b/modules/nf-core/gatk4/mutect2/tests/main.nf.test
index aea8d226949e..b0e22144c674 100644
--- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test
+++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test
@@ -8,10 +8,13 @@ nextflow_process {
     tag "modules_nfcore"
     tag "gatk4"
     tag "gatk4/mutect2"
+    config "./nextflow.config"
 
-    test("tumor_normal_pair") {
-        config "./pair.config"
+    test("human - bam - tumor_normal_pair") {
         when {
+            params {
+                module_args = "--normal-sample normal"
+            }
             process {
             """
             input[0] = [
@@ -55,7 +58,7 @@ nextflow_process {
                 { assert process.success },
                 {
                     assert snapshot(
-                        process.out.vcf.collect { file(it[1]).getName() },
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                         process.out.tbi.collect { file(it[1]).getName() },
                         process.out.stats,
                         process.out.f1r2,
@@ -66,9 +69,12 @@ nextflow_process {
         }
     }
 
-    test("tumor_normal_pair_f1r2") {
-        config "./f1r2.config"
+    test("human - bam - tumor_normal_pair_f1r2") {
+
         when {
+            params {
+                module_args = "--normal-sample normal --f1r2-tar-gz test.f1r2.tar.gz"
+            }
             process {
             """
             input[0] = [
@@ -111,7 +117,7 @@ nextflow_process {
                 { assert process.success },
                 {
                     assert snapshot(
-                        process.out.vcf.collect { file(it[1]).getName() },
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                         process.out.tbi.collect { file(it[1]).getName() },
                         process.out.stats,
                         process.out.f1r2.collect { file(it[1]).getName() },
@@ -121,8 +127,11 @@ nextflow_process {
             )
         }
     }
-    test("tumor_single"){
+    test("human - bam - tumor_only"){
         when {
+            params {
+                module_args = ''
+            }
             process {
             """
             input[0] = [
@@ -155,7 +164,7 @@ nextflow_process {
                 { assert process.success },
                 {
                     assert snapshot(
-                        process.out.vcf.collect { file(it[1]).getName() },
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                         process.out.tbi.collect { file(it[1]).getName() },
                         process.out.stats,
                         process.out.f1r2,
@@ -165,8 +174,11 @@ nextflow_process {
             )
         }
     }
-    test("cram_input"){
+    test("human - cram"){
         when {
+            params {
+                module_args = ''
+            }
             process{
             """
             input[0] = [
@@ -199,7 +211,7 @@ nextflow_process {
                 { assert process.success },
                 {
                     assert snapshot(
-                        process.out.vcf.collect { file(it[1]).getName() },
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                         process.out.tbi.collect { file(it[1]).getName() },
                         process.out.stats,
                         process.out.f1r2,
@@ -210,8 +222,11 @@ nextflow_process {
         }
     }
 
-    test("generate_pon") {
+    test("human - bam - generate_pon") {
         when {
+            params {
+                module_args = ''
+            }
             process {
             """
             input[0] = [
@@ -244,7 +259,7 @@ nextflow_process {
                 { assert process.success },
                 {
                     assert snapshot(
-                        process.out.vcf.collect { file(it[1]).getName() },
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                         process.out.tbi.collect { file(it[1]).getName() },
                         process.out.stats,
                         process.out.f1r2,
@@ -255,8 +270,11 @@ nextflow_process {
         }
     }
 
-    test("mitochondria"){
+    test("mitochondria - bam"){
         when {
+            params {
+                module_args = "--mitochondria-mode"
+            }
             process {
             """
             input[0] = [
@@ -289,7 +307,7 @@ nextflow_process {
                 { assert process.success },
                 {
                     assert snapshot(
-                        process.out.vcf.collect { file(it[1]).getName() },
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                         process.out.tbi.collect { file(it[1]).getName() },
                         process.out.stats,
                         process.out.f1r2,
@@ -300,9 +318,14 @@ nextflow_process {
         }
     }
 
-    test("tumor_normal_pair_f1r2_stubs"){
-        options "-stub-run"
+    test("human - bam - tumor_normal_pair_f1r2 - stub"){
+
+        options "-stub"
+
         when {
+            params {
+                module_args = ''
+            }
             process {
             """
             input[0] = [
@@ -343,15 +366,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                {
-                    assert snapshot(
-                        process.out.vcf.collect { file(it[1]).getName() },
-                        process.out.tbi.collect { file(it[1]).getName() },
-                        process.out.stats.collect { file(it[1]).getName() },
-                        process.out.f1r2.collect { file(it[1]).getName() },
-                        process.out.versions.collect { file(it[1]).getName() }
-                    ).match()
-                }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap
index b37450f4f47a..80d07bccbe73 100644
--- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap
@@ -1,33 +1,7 @@
 {
-    "tumor_normal_pair_f1r2_stubs": {
+    "human - bam - generate_pon": {
         "content": [
-            [
-                "test.vcf.gz"
-            ],
-            [
-                "test.vcf.gz.tbi"
-            ],
-            [
-                "test.vcf.gz.stats"
-            ],
-            [
-                "test.f1r2.tar.gz"
-            ],
-            [
-                "w"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-10-31T11:49:16.64829295"
-    },
-    "generate_pon": {
-        "content": [
-            [
-                "test.vcf.gz"
-            ],
+            "876aa6be01c0c8fc71ad8e99ed842240",
             [
                 "test.vcf.gz.tbi"
             ],
@@ -47,16 +21,14 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-31T11:48:44.796786166"
+        "timestamp": "2025-04-08T15:44:32.616294519"
     },
-    "mitochondria": {
+    "human - cram": {
         "content": [
-            [
-                "test.vcf.gz"
-            ],
+            "1b65f1a163b517944bf2e4b74230e035",
             [
                 "test.vcf.gz.tbi"
             ],
@@ -65,7 +37,7 @@
                     {
                         "id": "test"
                     },
-                    "test.vcf.gz.stats:md5,4f77301a125913170b8e9e7828b4ca3f"
+                    "test.vcf.gz.stats:md5,55ed641e16089afb33cdbc478e202d3d"
                 ]
             ],
             [
@@ -76,16 +48,14 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-31T11:49:03.399442766"
+        "timestamp": "2025-04-08T15:42:27.117032089"
     },
-    "cram_input": {
+    "mitochondria - bam": {
         "content": [
-            [
-                "test.vcf.gz"
-            ],
+            "ea70f79e33805a2c0b47b32a48a8d26f",
             [
                 "test.vcf.gz.tbi"
             ],
@@ -94,7 +64,7 @@
                     {
                         "id": "test"
                     },
-                    "test.vcf.gz.stats:md5,55ed641e16089afb33cdbc478e202d3d"
+                    "test.vcf.gz.stats:md5,fc6ea14ca2da346babe78161beea28c9"
                 ]
             ],
             [
@@ -105,25 +75,25 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-31T11:45:49.212101867"
+        "timestamp": "2025-04-08T15:44:46.867520687"
     },
-    "tumor_single": {
+    "human - bam - tumor_normal_pair": {
         "content": [
-            [
-                "test.vcf.gz"
-            ],
+            "7418ed45a029394253817a5eb7149334",
             [
                 "test.vcf.gz.tbi"
             ],
             [
                 [
                     {
-                        "id": "test"
+                        "id": "test",
+                        "normal_id": "normal",
+                        "tumor_id": "tumour"
                     },
-                    "test.vcf.gz.stats:md5,55ed641e16089afb33cdbc478e202d3d"
+                    "test.vcf.gz.stats:md5,17d2091015d04cbd4a26b7a67dc659e6"
                 ]
             ],
             [
@@ -134,27 +104,23 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-31T11:42:47.335589964"
+        "timestamp": "2025-04-08T16:02:48.334206829"
     },
-    "tumor_normal_pair": {
+    "human - bam - tumor_only": {
         "content": [
-            [
-                "test.vcf.gz"
-            ],
+            "1b65f1a163b517944bf2e4b74230e035",
             [
                 "test.vcf.gz.tbi"
             ],
             [
                 [
                     {
-                        "id": "test",
-                        "normal_id": "normal",
-                        "tumor_id": "tumour"
+                        "id": "test"
                     },
-                    "test.vcf.gz.stats:md5,17d2091015d04cbd4a26b7a67dc659e6"
+                    "test.vcf.gz.stats:md5,55ed641e16089afb33cdbc478e202d3d"
                 ]
             ],
             [
@@ -165,16 +131,111 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-31T11:36:10.506528759"
+        "timestamp": "2025-04-08T15:40:12.534802185"
     },
-    "tumor_normal_pair_f1r2": {
+    "human - bam - tumor_normal_pair_f1r2 - stub": {
         "content": [
-            [
-                "test.vcf.gz"
-            ],
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.f1r2.tar.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4"
+                ],
+                "f1r2": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.f1r2.tar.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "normal_id": "normal",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-08T15:44:59.443047344"
+    },
+    "human - bam - tumor_normal_pair_f1r2": {
+        "content": [
+            "7418ed45a029394253817a5eb7149334",
             [
                 "test.vcf.gz.tbi"
             ],
@@ -196,9 +257,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-31T11:39:21.909639821"
+        "timestamp": "2025-04-08T16:25:12.434872797"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/mutect2/tests/mito.config b/modules/nf-core/gatk4/mutect2/tests/mito.config
deleted file mode 100644
index de61d3e24350..000000000000
--- a/modules/nf-core/gatk4/mutect2/tests/mito.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
-    ext.args = { "--mitochondria-mode" }
-}
diff --git a/modules/nf-core/gatk4/mutect2/tests/nextflow.config b/modules/nf-core/gatk4/mutect2/tests/nextflow.config
new file mode 100644
index 000000000000..08e942851735
--- /dev/null
+++ b/modules/nf-core/gatk4/mutect2/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_MUTECT2 {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/gatk4/mutect2/tests/pair.config b/modules/nf-core/gatk4/mutect2/tests/pair.config
deleted file mode 100644
index 2a812b8254f7..000000000000
--- a/modules/nf-core/gatk4/mutect2/tests/pair.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
-    ext.args = { "--normal-sample $meta.normal_id" }
-}
diff --git a/modules/nf-core/gatk4spark/applybqsr/main.nf b/modules/nf-core/gatk4spark/applybqsr/main.nf
index abd4c9946e96..da17760967ca 100644
--- a/modules/nf-core/gatk4spark/applybqsr/main.nf
+++ b/modules/nf-core/gatk4spark/applybqsr/main.nf
@@ -1,22 +1,22 @@
 process GATK4SPARK_APPLYBQSR {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0':
-        'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0'
+        : 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0'}"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
-    path  fasta
-    path  fai
-    path  dict
+    path fasta
+    path fai
+    path dict
 
     output:
-    tuple val(meta), path("${prefix}.bam") , emit: bam,  optional: true
+    tuple val(meta), path("${prefix}.bam"),  emit: bam,  optional: true
     tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true
-    path "versions.yml"            , emit: versions
+    path "versions.yml",                     emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,26 +24,27 @@ process GATK4SPARK_APPLYBQSR {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    def interval_command = intervals ? "--intervals $intervals" : ""
+    def interval_command = intervals ? "--intervals ${intervals}" : ""
 
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[GATK ApplyBQSRSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        log.info('[GATK ApplyBQSRSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
+    }
+    else {
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
     """
     gatk \\
         --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
         ApplyBQSRSpark \\
-        --input $input \\
+        --input ${input} \\
         --output ${prefix}.${input.getExtension()} \\
-        --reference $fasta \\
-        --bqsr-recal-file $bqsr_table \\
-        $interval_command \\
+        --reference ${fasta} \\
+        --bqsr-recal-file ${bqsr_table} \\
+        ${interval_command} \\
         --spark-master local[${task.cpus}] \\
         --tmp-dir . \\
-        $args
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test
index 53f202161321..25284c769cbb 100644
--- a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test
+++ b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test
@@ -17,27 +17,62 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
                     []
                 ]
-                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [],
+                    [],
+                    [],
+                    []
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
 
     }
 
+
     test("sarscov2 - bam intervals") {
 
         when {
@@ -45,28 +80,30 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
-    test("sarscov2 - bam - stub") {
+    test("sarscov2 - bam intervals -stub") {
         options "-stub"
 
         when {
@@ -74,25 +111,27 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    [],
-                    [],
-                    [],
-                    []
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                 ]
-                input[1] = []
-                input[2] = []
-                input[3] = []
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
     test("sarscov2 - cram") {
@@ -102,26 +141,57 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-                input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-                input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
+    test("sarscov2 - cram -stub") {
+        options "-stub"
 
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap
index 4af457d39f28..cd2a088c7362 100644
--- a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap
@@ -40,13 +40,18 @@
                 "versions": [
                     "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
                 ]
+            },
+            {
+                "GATK4SPARK_APPLYBQSR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-17T16:50:02.397152291"
+        "timestamp": "2025-04-11T14:56:27.915627809"
     },
     "sarscov2 - cram": {
         "content": [
@@ -79,13 +84,72 @@
                 "versions": [
                     "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
                 ]
+            },
+            {
+                "GATK4SPARK_APPLYBQSR": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T14:57:42.699756036"
+    },
+    "sarscov2 - cram -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
+                ]
+            },
+            {
+                "GATK4SPARK_APPLYBQSR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-17T16:50:30.685886937"
+        "timestamp": "2025-04-11T14:57:58.189642524"
     },
     "sarscov2 - bam": {
         "content": [
@@ -118,13 +182,18 @@
                 "versions": [
                     "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
                 ]
+            },
+            {
+                "GATK4SPARK_APPLYBQSR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-17T16:49:26.18719288"
+        "timestamp": "2025-04-11T14:56:13.425170564"
     },
     "sarscov2 - bam intervals": {
         "content": [
@@ -157,12 +226,71 @@
                 "versions": [
                     "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
                 ]
+            },
+            {
+                "GATK4SPARK_APPLYBQSR": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T14:56:55.562307069"
+    },
+    "sarscov2 - bam intervals -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,985dcafacddb7013ec01b73fd9163290"
+                ]
+            },
+            {
+                "GATK4SPARK_APPLYBQSR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-17T16:49:49.844595108"
+        "timestamp": "2025-04-11T14:57:11.97218192"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gatk4spark/baserecalibrator/main.nf b/modules/nf-core/gatk4spark/baserecalibrator/main.nf
index 304b1bc5240f..1f9e2cb595f6 100644
--- a/modules/nf-core/gatk4spark/baserecalibrator/main.nf
+++ b/modules/nf-core/gatk4spark/baserecalibrator/main.nf
@@ -1,23 +1,23 @@
 process GATK4SPARK_BASERECALIBRATOR {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0':
-        'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0'
+        : 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0'}"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
-    path  fasta
-    path  fai
-    path  dict
-    path  known_sites
-    path  known_sites_tbi
+    path fasta
+    path fai
+    path dict
+    path known_sites
+    path known_sites_tbi
 
     output:
     tuple val(meta), path("*.table"), emit: table
-    path "versions.yml"             , emit: versions
+    path "versions.yml",              emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,26 +25,27 @@ process GATK4SPARK_BASERECALIBRATOR {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def interval_command = intervals ? "--intervals $intervals" : ""
-    def sites_command = known_sites.collect{"--known-sites $it"}.join(' ')
+    def interval_command = intervals ? "--intervals ${intervals}" : ""
+    def sites_command = known_sites.collect { "--known-sites ${it}" }.join(' ')
 
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[GATK BaseRecalibratorSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        log.info('[GATK BaseRecalibratorSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
+    }
+    else {
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
     """
     gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
         BaseRecalibratorSpark \\
-        --input $input \\
+        --input ${input} \\
         --output ${prefix}.table \\
-        --reference $fasta \\
-        $interval_command \\
-        $sites_command \\
+        --reference ${fasta} \\
+        ${interval_command} \\
+        ${sites_command} \\
         --spark-master local[${task.cpus}] \\
         --tmp-dir . \\
-        $args
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test
index ff6867d2f244..6bb4d9dd01a6 100644
--- a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test
+++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test
@@ -14,147 +14,255 @@ nextflow_process {
         when {
             process {
                 """
-                input_bam = [ [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
-                ]
-                fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-                sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-                sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-
-                input = [input_bam, fasta, fai, dict, sites, sites_tbi]
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true))
+                input[5] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true))
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
     test("homo sapiens - cram") {
         when {
             process {
                 """
-                input_cram = [ [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
                     []
-                ]
-                fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-                fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-                dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-                sites = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true)
-                sites_tbi = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true)
-
-                input = [input_cram, fasta, fai, dict, sites, sites_tbi]
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true))
+                input[5] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true))
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
     test("sarscov2 - bam - intervals") {
         when {
             process {
                 """
-                input_bam = [ [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-                ]
-                fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-                sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-                sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-
-                input = [input_bam, fasta, fai, dict, sites, sites_tbi]
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true))
+                input[5] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true))
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
     test("sarscov2 - bam - multi sites") {
         when {
             process {
                 """
-                input_bam = [ [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
-                ]
-                fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-                sites = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)]
-                sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)]
-                input = [input_bam, fasta, fai, dict, sites, sites_tbi]
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+                ])
+                input[5] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ])
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
-    test("sarscov2 - bam - stub") {
-
+    test("sarscov2 - bam -stub") {
         options "-stub"
-
         when {
             process {
                 """
-                input_bam = [ [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
-                ]
-                fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-                sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-                sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true))
+                input[5] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true))
+                """
+            }
+        }
 
-                input = [input_bam, fasta, fai, dict, sites, sites_tbi]
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+    test("homo sapiens - cram -stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                    []
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true))
+                input[5] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true))
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
+    }
+
+    test("sarscov2 - bam - intervals -stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true))
+                input[5] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true))
+                """
+            }
+        }
 
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
     }
 
+    test("sarscov2 - bam - multi sites -stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    []
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true))
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true))
+                input[4] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+                ])
+                input[5] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap
index c02ce4b1c8e3..28394ad3db63 100644
--- a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "sarscov2 - bam - multi sites": {
+    "sarscov2 - bam - intervals -stub": {
         "content": [
             {
                 "0": [
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7"
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -18,21 +18,26 @@
                         {
                             "id": "test"
                         },
-                        "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7"
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
                 ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:52:50.311106222"
+        "timestamp": "2025-04-11T15:00:38.617564388"
     },
-    "sarscov2 - bam - stub": {
+    "sarscov2 - bam - multi sites": {
         "content": [
             {
                 "0": [
@@ -40,7 +45,7 @@
                         {
                             "id": "test"
                         },
-                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7"
                     ]
                 ],
                 "1": [
@@ -51,19 +56,24 @@
                         {
                             "id": "test"
                         },
-                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
                 ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:38:35.054385124"
+        "timestamp": "2025-04-11T14:59:50.213616922"
     },
     "homo sapiens - cram": {
         "content": [
@@ -90,13 +100,18 @@
                 "versions": [
                     "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
                 ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T12:03:12.23567219"
+        "timestamp": "2025-04-11T14:58:59.091441241"
     },
     "sarscov2 - bam - intervals": {
         "content": [
@@ -123,13 +138,18 @@
                 "versions": [
                     "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
                 ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:51:34.077518575"
+        "timestamp": "2025-04-11T14:59:24.000377035"
     },
     "sarscov2 - bam": {
         "content": [
@@ -156,12 +176,131 @@
                 "versions": [
                     "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
                 ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T14:58:25.814297279"
+    },
+    "sarscov2 - bam - multi sites -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
+                ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T15:00:55.024158381"
+    },
+    "sarscov2 - bam -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
+                ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T15:00:05.696488985"
+    },
+    "homo sapiens - cram -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58"
+                ]
+            },
+            {
+                "GATK4SPARK_BASERECALIBRATOR": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:49:36.893419883"
+        "timestamp": "2025-04-11T15:00:21.556918585"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gatk4spark/markduplicates/main.nf b/modules/nf-core/gatk4spark/markduplicates/main.nf
index 9cb74c8b3639..a0dcf3fee4a1 100644
--- a/modules/nf-core/gatk4spark/markduplicates/main.nf
+++ b/modules/nf-core/gatk4spark/markduplicates/main.nf
@@ -1,23 +1,23 @@
 process GATK4SPARK_MARKDUPLICATES {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0':
-        'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0'
+        : 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0'}"
 
     input:
     tuple val(meta), path(bam)
-    path  fasta
-    path  fasta_fai
-    path  dict
+    path fasta
+    path fasta_fai
+    path dict
 
     output:
     tuple val(meta), path("${prefix}"),     emit: output
-    tuple val(meta), path("${prefix}.bai"), emit: bam_index, optional:true
-    tuple val(meta), path("*.metrics"),     emit: metrics, optional: true
-    path "versions.yml"               ,     emit: versions
+    tuple val(meta), path("${prefix}.bai"), emit: bam_index, optional: true
+    tuple val(meta), path("*.metrics"),     emit: metrics,   optional: true
+    path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,23 +25,24 @@ process GATK4SPARK_MARKDUPLICATES {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}.bam"
-    def input_list = bam.collect{"--input $it"}.join(' ')
+    def input_list = bam.collect { "--input ${it}" }.join(' ')
 
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        log.info('[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
+    }
+    else {
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
     """
     gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
         MarkDuplicatesSpark \\
-        $input_list \\
-        --output $prefix \\
-        --reference $fasta \\
+        ${input_list} \\
+        --output ${prefix} \\
+        --reference ${fasta} \\
         --spark-master local[${task.cpus}] \\
         --tmp-dir . \\
-        $args
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -55,6 +56,7 @@ process GATK4SPARK_MARKDUPLICATES {
     touch ${prefix}
     touch ${prefix}.bai
     touch ${prefix}.metrics
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
diff --git a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test
index 2aa2db69ed98..40dbb713a00b 100644
--- a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test
+++ b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test
@@ -17,23 +17,25 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
     test("homo_sapiens - bam - multiple") {
@@ -43,26 +45,28 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test', single_end:false ],
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam', checkIfExists: true)
                     ]
                 ]
-                input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-                input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-                input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
     test("homo_sapiens - bam - metrics") {
@@ -72,30 +76,33 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test', single_end:false ],
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam', checkIfExists: true)
                     ]
                 ]
-                input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-                input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-                input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.versions).match("homo_sapiens - bam - metrics - versions") },
-                { assert snapshot(process.out.output).match("homo_sapiens - bam - metrics - output") },
-                { assert snapshot(process.out.bam_index).match("homo_sapiens - bam - metrics - bam_index") },
-                { assert path(process.out.metrics[0][1]).readLines()[5].contains("GATKDuplicationMetrics") },
-                { assert path(process.out.metrics[0][1]).readLines().size() == 11 }
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.output,
+                    process.out.bam_index,
+                    path(process.out.metrics[0][1]).readLines()[5],
+                    path(process.out.metrics[0][1]).readLines().size(),
+                    path(process.out.versions[0]).yaml
+                    )
+                }
             )
         }
-
     }
 
     test("homo_sapiens - cram") {
@@ -105,54 +112,152 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test', single_end:false ],
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam', checkIfExists: true)
                     ]
                 ]
-                input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-                input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-                input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
-
     }
 
-    test("stub") {
+    test("sarscov2 - bam -stub") {
+        options "-stub"
         config "./bam.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.name.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - bam - multiple -stub") {
         options "-stub"
+        config "./bam.config"
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    []
+                    [ id:'test', single_end:false ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam', checkIfExists: true)
+                    ]
                 ]
-                input[1] = []
-                input[2] = []
-                input[3] = []
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
+    }
+
+    test("homo_sapiens - bam - metrics -stub") {
+        options "-stub"
+        config "./metrics.config"
 
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
     }
 
+    test("homo_sapiens - cram -stub") {
+        options "-stub"
+        config "./cram.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+                """
+            }
+        }
 
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap
index f9366caead2b..1482578a1c24 100644
--- a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap
@@ -50,31 +50,18 @@
                 "versions": [
                     "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
                 ]
+            },
+            {
+                "GATK4SPARK_MARKDUPLICATES": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-06T11:52:48.84070018"
-    },
-    "homo_sapiens - bam - metrics - output": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.bam:md5,1154a16717d430199f3e9994a87b546a"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-02-15T11:53:32.254055925"
+        "timestamp": "2025-04-11T15:01:54.825208573"
     },
     "homo_sapiens - cram": {
         "content": [
@@ -115,45 +102,96 @@
                 "versions": [
                     "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
                 ]
+            },
+            {
+                "GATK4SPARK_MARKDUPLICATES": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-06T11:54:09.554533288"
-    },
-    "homo_sapiens - bam - metrics - versions": {
-        "content": [
-            [
-                "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:53:39.648663125"
+        "timestamp": "2025-04-11T15:03:51.19014784"
     },
-    "homo_sapiens - bam - metrics - bam_index": {
+    "homo_sapiens - bam - metrics -stub": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.bam.bai:md5,d947dccacf3fb7fcf174d364a5f7856d"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
+                ],
+                "bam_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
                 ]
-            ]
+            },
+            {
+                "GATK4SPARK_MARKDUPLICATES": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-02-15T11:53:32.305216975"
+        "timestamp": "2025-04-11T15:05:23.678812172"
     },
-    "stub": {
+    "homo_sapiens - bam - multiple -stub": {
         "content": [
             {
                 "0": [
@@ -216,13 +254,94 @@
                 "versions": [
                     "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
                 ]
+            },
+            {
+                "GATK4SPARK_MARKDUPLICATES": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:54:21.987287007"
+        "timestamp": "2025-04-11T15:04:49.498784821"
+    },
+    "homo_sapiens - cram -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
+                ],
+                "bam_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
+                ]
+            },
+            {
+                "GATK4SPARK_MARKDUPLICATES": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T15:05:56.744218653"
     },
     "sarscov2 - bam": {
         "content": [
@@ -275,12 +394,93 @@
                 "versions": [
                     "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
                 ]
+            },
+            {
+                "GATK4SPARK_MARKDUPLICATES": {
+                    "gatk4": "4.6.1.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T15:01:22.411041697"
+    },
+    "sarscov2 - bam -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
+                ],
+                "bam_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94"
+                ]
+            },
+            {
+                "GATK4SPARK_MARKDUPLICATES": {
+                    "gatk4": "4.6.1.0"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-11-06T11:51:28.270175346"
+        "timestamp": "2025-04-11T15:04:15.984302135"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gem2/gem2bedmappability/main.nf b/modules/nf-core/gem2/gem2bedmappability/main.nf
index 0fb84599ffae..fab457596a65 100644
--- a/modules/nf-core/gem2/gem2bedmappability/main.nf
+++ b/modules/nf-core/gem2/gem2bedmappability/main.nf
@@ -21,7 +21,7 @@ process GEM2_GEM2BEDMAPPABILITY {
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = '20200110' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     gem-2-bed mappability \\
@@ -36,8 +36,7 @@ process GEM2_GEM2BEDMAPPABILITY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = '20200110' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
diff --git a/modules/nf-core/gem2/gem2bedmappability/tests/main.nf.test b/modules/nf-core/gem2/gem2bedmappability/tests/main.nf.test
new file mode 100644
index 000000000000..e4998c90c9f0
--- /dev/null
+++ b/modules/nf-core/gem2/gem2bedmappability/tests/main.nf.test
@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process GEM2_GEM2BEDMAPPABILITY"
+    script "../main.nf"
+    process "GEM2_GEM2BEDMAPPABILITY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gem2"
+    tag "gem2/gem2bedmappability"
+    tag "gem2/gemmappability"
+    tag "gem2/gemindexer"
+
+    setup {
+        run("GEM2_GEMINDEXER") {
+            script "../../gemindexer/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta',checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        run("GEM2_GEMMAPPABILITY") {
+            script "../../gemmappability/main.nf"
+
+            process {
+                """
+                input[0] = GEM2_GEMINDEXER.out.index
+                input[1] = "100"
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - map index") {
+
+        when {
+            process {
+                """
+                input[0] = GEM2_GEMMAPPABILITY.out.map
+                input[1] = GEM2_GEMINDEXER.out.index
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("sarscov2 - map index -- stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = GEM2_GEMMAPPABILITY.out.map
+                input[1] = GEM2_GEMINDEXER.out.index
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gem2/gem2bedmappability/tests/main.nf.test.snap b/modules/nf-core/gem2/gem2bedmappability/tests/main.nf.test.snap
new file mode 100644
index 000000000000..1070ef2a4cf4
--- /dev/null
+++ b/modules/nf-core/gem2/gem2bedmappability/tests/main.nf.test.snap
@@ -0,0 +1,113 @@
+{
+    "sarscov2 - map index": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bg:md5,42596230d57c308892bcaefb3eabbf1b"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sizes:md5,58102c0866e0bc69831c94d02fd859e1"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,25751db13de2d20099e2dcc8ba82e7da"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bg:md5,42596230d57c308892bcaefb3eabbf1b"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sizes:md5,58102c0866e0bc69831c94d02fd859e1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,25751db13de2d20099e2dcc8ba82e7da"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T14:26:31.503481693"
+    },
+    "sarscov2 - map index -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,25751db13de2d20099e2dcc8ba82e7da"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,25751db13de2d20099e2dcc8ba82e7da"
+                ]
+            },
+            {
+                "GEM2_GEM2BEDMAPPABILITY": {
+                    "gem2": 20200110
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T14:26:37.569803264"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gem2/gemmappability/main.nf b/modules/nf-core/gem2/gemmappability/main.nf
index 37ecb375d865..ebf619476e08 100644
--- a/modules/nf-core/gem2/gemmappability/main.nf
+++ b/modules/nf-core/gem2/gemmappability/main.nf
@@ -20,8 +20,8 @@ process GEM2_GEMMAPPABILITY {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args    = task.ext.args   ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = '20200110' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     gem-mappability \\
@@ -38,8 +38,7 @@ process GEM2_GEMMAPPABILITY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = '20200110' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
diff --git a/modules/nf-core/gem2/gemmappability/tests/main.nf.test b/modules/nf-core/gem2/gemmappability/tests/main.nf.test
new file mode 100644
index 000000000000..703620dd750a
--- /dev/null
+++ b/modules/nf-core/gem2/gemmappability/tests/main.nf.test
@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process GEM2_GEMMAPPABILITY"
+    script "../main.nf"
+    process "GEM2_GEMMAPPABILITY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gem2"
+    tag "gem2/gemmappability"
+    tag "gem2/gemindexer"
+
+    setup {
+        run("GEM2_GEMINDEXER") {
+            script "../../gemindexer/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta',checkIfExists:true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = GEM2_GEMINDEXER.out.index
+                input[1] = "100"
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("sarscov2 - fasta -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = GEM2_GEMINDEXER.out.index
+                input[1] = "100"
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gem2/gemmappability/tests/main.nf.test.snap b/modules/nf-core/gem2/gemmappability/tests/main.nf.test.snap
new file mode 100644
index 000000000000..56f00d7f24dc
--- /dev/null
+++ b/modules/nf-core/gem2/gemmappability/tests/main.nf.test.snap
@@ -0,0 +1,77 @@
+{
+    "sarscov2 - fasta -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ],
+                "map": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ]
+            },
+            {
+                "GEM2_GEMMAPPABILITY": {
+                    "gem2": 20200110
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T15:41:25.596792189"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,8380b048fec0e8c4f104f49d2bf784c4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ],
+                "map": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,8380b048fec0e8c4f104f49d2bf784c4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T15:40:30.596290605"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genescopefk/main.nf b/modules/nf-core/genescopefk/main.nf
index c257a0efdaee..799153b6150b 100644
--- a/modules/nf-core/genescopefk/main.nf
+++ b/modules/nf-core/genescopefk/main.nf
@@ -27,24 +27,43 @@ process GENESCOPEFK {
         error "GENESCOPEFK module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def GENESCOPE_VERSION = '380815c420f50171f9234a0fd1ff426b39829b91' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
-    #! /usr/bin/env bash
-
     GeneScopeFK.R \\
         $args \\
         --input $fastk_histex_histogram \\
         --output . \\
         --name_prefix ${prefix}
 
-    printf -v KMERCOV "%.2f\\n" \$( grep "^kmercov" *_model.txt | cut -d" " -f2 )
+    printf -v KMERCOV "%.2f" \$( grep "^kmercov" *_model.txt | cut -d" " -f2 )
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genescopefk: $GENESCOPE_VERSION
+        r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def GENESCOPE_VERSION = '380815c420f50171f9234a0fd1ff426b39829b91'
+    """
+    touch "${prefix}_linear_plot.png"
+    touch "${prefix}_log_plot.png"
+    touch "${prefix}_model.txt"
+    touch "${prefix}_summary.txt"
+    touch "${prefix}_transformed_linear_plot.png"
+    touch "${prefix}_transformed_log_plot.png"
+
+    printf -v KMERCOV "%.2f" \$( grep "^kmercov" *_model.txt | cut -d" " -f2 )
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        genescope: $GENESCOPE_VERSION
+        genescopefk: $GENESCOPE_VERSION
         r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
     END_VERSIONS
     """
+
 }
diff --git a/modules/nf-core/genescopefk/tests/main.nf.test b/modules/nf-core/genescopefk/tests/main.nf.test
new file mode 100644
index 000000000000..8411a7024b3a
--- /dev/null
+++ b/modules/nf-core/genescopefk/tests/main.nf.test
@@ -0,0 +1,83 @@
+nextflow_process {
+
+    name "Test Process GENESCOPEFK"
+    config "./nextflow.config"
+    script "../main.nf"
+    process "GENESCOPEFK"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fastk"
+    tag "fastk/fastk"
+    tag "fastk/histex"
+    tag "genescopefk"
+
+    setup {
+        run("FASTK_FASTK") {
+            script "../../fastk/fastk/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test', single_end:true],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz',checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        run("FASTK_HISTEX") {
+            script "../../fastk/histex/main.nf"
+
+            process {
+                """
+                input[0] = FASTK_FASTK.out.hist
+                """
+            }
+        }
+    }
+
+    test("homo_sapiens - hist") {
+        when {
+            params {
+                fastk_histex_arg = "-G"
+                genescopefk_arg  = "--kmer_length 40 --ploidy 1"
+            }
+            process {
+                """
+                input[0] = FASTK_HISTEX.out.hist
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - hist -- stub") {
+        options '-stub'
+        when {
+            params {
+                fastk_histex_arg = "-G"
+                genescopefk_arg  = "--kmer_length 40 --ploidy 1"
+            }
+            process {
+                """
+                input[0] = FASTK_HISTEX.out.hist
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genescopefk/tests/main.nf.test.snap b/modules/nf-core/genescopefk/tests/main.nf.test.snap
new file mode 100644
index 000000000000..8b6e68e7bdc5
--- /dev/null
+++ b/modules/nf-core/genescopefk/tests/main.nf.test.snap
@@ -0,0 +1,318 @@
+{
+    "homo_sapiens - hist": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_linear_plot.png:md5,bb221e2e21a6c0d04dcb6ec8f1bf1cd7",
+                            "test_transformed_linear_plot.png:md5,3c8e3ad315e6c15cdf51c87de277ec1f"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_log_plot.png:md5,d71ad0c963775992043c8f3c55d27fc4",
+                            "test_transformed_log_plot.png:md5,90d983c6faa9b8a02a1d26b777feefc6"
+                        ]
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_model.txt:md5,49e5a66cf02b53a3b20880bfabef2ee8"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_summary.txt:md5,34540dcc2ba4ab9530f8878bbdc0921c"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_linear_plot.png:md5,3c8e3ad315e6c15cdf51c87de277ec1f"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_log_plot.png:md5,90d983c6faa9b8a02a1d26b777feefc6"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "12.25"
+                    ]
+                ],
+                "7": [
+                    "versions.yml:md5,de2e6adb831619dff8e2e7262736ba5a"
+                ],
+                "kmer_cov": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "12.25"
+                    ]
+                ],
+                "linear_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_linear_plot.png:md5,bb221e2e21a6c0d04dcb6ec8f1bf1cd7",
+                            "test_transformed_linear_plot.png:md5,3c8e3ad315e6c15cdf51c87de277ec1f"
+                        ]
+                    ]
+                ],
+                "log_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_log_plot.png:md5,d71ad0c963775992043c8f3c55d27fc4",
+                            "test_transformed_log_plot.png:md5,90d983c6faa9b8a02a1d26b777feefc6"
+                        ]
+                    ]
+                ],
+                "model": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_model.txt:md5,49e5a66cf02b53a3b20880bfabef2ee8"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_summary.txt:md5,34540dcc2ba4ab9530f8878bbdc0921c"
+                    ]
+                ],
+                "transformed_linear_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_linear_plot.png:md5,3c8e3ad315e6c15cdf51c87de277ec1f"
+                    ]
+                ],
+                "transformed_log_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_log_plot.png:md5,90d983c6faa9b8a02a1d26b777feefc6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,de2e6adb831619dff8e2e7262736ba5a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T15:34:21.631389751"
+    },
+    "homo_sapiens - hist -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_linear_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_transformed_linear_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_log_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_transformed_log_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_model.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_linear_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_log_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "0.00"
+                    ]
+                ],
+                "7": [
+                    "versions.yml:md5,de2e6adb831619dff8e2e7262736ba5a"
+                ],
+                "kmer_cov": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "0.00"
+                    ]
+                ],
+                "linear_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_linear_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_transformed_linear_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "log_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_log_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_transformed_log_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "model": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_model.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "transformed_linear_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_linear_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "transformed_log_plot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_transformed_log_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,de2e6adb831619dff8e2e7262736ba5a"
+                ]
+            },
+            {
+                "GENESCOPEFK": {
+                    "genescopefk": "380815c420f50171f9234a0fd1ff426b39829b91",
+                    "r": "4.2.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T15:05:55.106012575"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genescopefk/tests/nextflow.config b/modules/nf-core/genescopefk/tests/nextflow.config
new file mode 100644
index 000000000000..4bee9abd8922
--- /dev/null
+++ b/modules/nf-core/genescopefk/tests/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: FASTK_HISTEX {
+        ext.args  = params.fastk_histex_arg
+    }
+
+    withName: GENESCOPEFK {
+        ext.args  = params.genescopefk_arg
+    }
+}
diff --git a/modules/nf-core/genmap/map/main.nf b/modules/nf-core/genmap/map/main.nf
index c506c84f717d..e9b600894072 100644
--- a/modules/nf-core/genmap/map/main.nf
+++ b/modules/nf-core/genmap/map/main.nf
@@ -22,9 +22,9 @@ process GENMAP_MAP {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "$meta.id"
-    def bed = regions ? "--selection ${regions}" : ""
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_map"
+    def bed    = regions ? "--selection ${regions}" : ""
 
     if ("$index" == "${prefix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
@@ -43,13 +43,13 @@ process GENMAP_MAP {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "$meta.id"
+    def args       = task.ext.args   ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}_map"
     def token_args = args.tokenize(" ")
-    def wig = token_args.contains("-w") || token_args.contains("--wig") ?       "touch ${prefix}.wig"       : ""
-    def bg =  token_args.contains("-bg") || token_args.contains("--bedgraph") ? "touch ${prefix}.bedgraph"  : ""
-    def txt = token_args.contains("-t") || token_args.contains("--txt") ?       "touch ${prefix}.txt"       : ""
-    def csv = token_args.contains("-d") || token_args.contains("--csv") ?       "touch ${prefix}.csv"       : ""
+    def wig = token_args.contains("-w")  || token_args.contains("--wig")      ? "touch ${prefix}.wig"       : ""
+    def bg  = token_args.contains("-bg") || token_args.contains("--bedgraph") ? "touch ${prefix}.bedgraph"  : ""
+    def txt = token_args.contains("-t")  || token_args.contains("--txt")      ? "touch ${prefix}.txt"       : ""
+    def csv = token_args.contains("-d")  || token_args.contains("--csv")      ? "touch ${prefix}.csv"       : ""
 
     if ("$index" == "${prefix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
diff --git a/modules/nf-core/genmap/map/tests/main.nf.test b/modules/nf-core/genmap/map/tests/main.nf.test
new file mode 100644
index 000000000000..508d98f4fa04
--- /dev/null
+++ b/modules/nf-core/genmap/map/tests/main.nf.test
@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process GENMAP_MAP"
+    config "./nextflow.config"
+    script "../main.nf"
+    process "GENMAP_MAP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "genmap"
+    tag "genmap/index"
+    tag "genmap/map"
+
+    setup {
+        run("GENMAP_INDEX") {
+            script "../../index/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - index bed") {
+
+        when {
+            params {
+                module_args   = "-K 50 -E 2 -w -t -bg -d"
+            }
+            process {
+                """
+                input[0] = GENMAP_INDEX.out.index.view()
+                input[1] = [
+                    [id:"bed"],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists:true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("sarscov2 - index bed -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args   = "-K 50 -E 2 -w -t -bg -d"
+            }
+            process {
+                """
+                input[0] = GENMAP_INDEX.out.index
+                input[1] = [
+                    [id:"bed"],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists:true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genmap/map/tests/main.nf.test.snap b/modules/nf-core/genmap/map/tests/main.nf.test.snap
new file mode 100644
index 000000000000..836e275b4367
--- /dev/null
+++ b/modules/nf-core/genmap/map/tests/main.nf.test.snap
@@ -0,0 +1,169 @@
+{
+    "sarscov2 - index bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.wig:md5,c940a5c35af6ac1c11ecc87b7662fc2a"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.bedgraph:md5,27ca54c920f3ff0c5985384e557a40f2"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.txt:md5,7f9aeaa3d174bb5e6f552efd4f857b4e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.csv:md5,4167a6c7ffbecc1a239c5c1e16b2cbc5"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.bedgraph:md5,27ca54c920f3ff0c5985384e557a40f2"
+                    ]
+                ],
+                "csv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.csv:md5,4167a6c7ffbecc1a239c5c1e16b2cbc5"
+                    ]
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.txt:md5,7f9aeaa3d174bb5e6f552efd4f857b4e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
+                ],
+                "wig": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.wig:md5,c940a5c35af6ac1c11ecc87b7662fc2a"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T16:10:45.401177409"
+    },
+    "sarscov2 - index bed -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
+                ],
+                "wig": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_map.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            },
+            {
+                "GENMAP_MAP": {
+                    "genmap": "1.3.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T16:10:51.374175856"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genmap/map/tests/nextflow.config b/modules/nf-core/genmap/map/tests/nextflow.config
new file mode 100644
index 000000000000..963e6e9c8a6a
--- /dev/null
+++ b/modules/nf-core/genmap/map/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "GENMAP_MAP" {
+        ext.args   = params.module_args
+    }
+}
diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml
index 163ddf093118..38153d167024 100644
--- a/modules/nf-core/genmod/annotate/environment.yml
+++ b/modules/nf-core/genmod/annotate/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.9
+  - bioconda::genmod=3.10
diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf
index 0b8b232de83f..f778d0d4c6d1 100644
--- a/modules/nf-core/genmod/annotate/main.nf
+++ b/modules/nf-core/genmod/annotate/main.nf
@@ -4,8 +4,8 @@ process GENMOD_ANNOTATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
-        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10--pyh7e72e81_0':
+        'biocontainers/genmod:3.10--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test.snap b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
index 402b5c01cf1a..16859b621812 100644
--- a/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
@@ -2,15 +2,15 @@
     "genmod_annotate": {
         "content": [
             [
-                "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+                "versions.yml:md5,a1e4c9528e1c03a40eb485ac8a89201d"
             ],
             "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:44:57.176895794"
+        "timestamp": "2025-04-11T15:36:56.251275862"
     },
     "genmod_annotate - stub": {
         "content": [
@@ -25,7 +25,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+                    "versions.yml:md5,a1e4c9528e1c03a40eb485ac8a89201d"
                 ],
                 "vcf": [
                     [
@@ -37,14 +37,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+                    "versions.yml:md5,a1e4c9528e1c03a40eb485ac8a89201d"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:49:16.409331019"
+        "timestamp": "2025-04-11T15:37:08.724847013"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml
index 163ddf093118..38153d167024 100644
--- a/modules/nf-core/genmod/compound/environment.yml
+++ b/modules/nf-core/genmod/compound/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.9
+  - bioconda::genmod=3.10
diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf
index ca6a22a1994d..e244c2eea8fd 100644
--- a/modules/nf-core/genmod/compound/main.nf
+++ b/modules/nf-core/genmod/compound/main.nf
@@ -4,8 +4,8 @@ process GENMOD_COMPOUND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
-        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10--pyh7e72e81_0':
+        'biocontainers/genmod:3.10--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test.snap b/modules/nf-core/genmod/compound/tests/main.nf.test.snap
index b114cc3310cf..282f7894d2c7 100644
--- a/modules/nf-core/genmod/compound/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/compound/tests/main.nf.test.snap
@@ -2,15 +2,15 @@
     "genmod_compound": {
         "content": [
             [
-                "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+                "versions.yml:md5,f27780c4f32e6a54d8199ab8b748c6aa"
             ],
             "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:49:41.417545149"
+        "timestamp": "2025-04-11T15:37:22.533444662"
     },
     "genmod_compound - stub": {
         "content": [
@@ -25,7 +25,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+                    "versions.yml:md5,f27780c4f32e6a54d8199ab8b748c6aa"
                 ],
                 "vcf": [
                     [
@@ -37,14 +37,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+                    "versions.yml:md5,f27780c4f32e6a54d8199ab8b748c6aa"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:49:48.678803012"
+        "timestamp": "2025-04-11T15:37:34.753562496"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml
index 163ddf093118..38153d167024 100644
--- a/modules/nf-core/genmod/models/environment.yml
+++ b/modules/nf-core/genmod/models/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.9
+  - bioconda::genmod=3.10
diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf
index a869221e9bed..ec4567f932cc 100644
--- a/modules/nf-core/genmod/models/main.nf
+++ b/modules/nf-core/genmod/models/main.nf
@@ -4,8 +4,8 @@ process GENMOD_MODELS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
-        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10--pyh7e72e81_0':
+        'biocontainers/genmod:3.10--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf), path (fam)
diff --git a/modules/nf-core/genmod/models/tests/main.nf.test.snap b/modules/nf-core/genmod/models/tests/main.nf.test.snap
index 7484a7fd0f98..54ead57fcbc2 100644
--- a/modules/nf-core/genmod/models/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/models/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+                    "versions.yml:md5,ea3c11abc1c5be5d8c0fd50ca4bb2344"
                 ],
                 "vcf": [
                     [
@@ -24,27 +24,27 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+                    "versions.yml:md5,ea3c11abc1c5be5d8c0fd50ca4bb2344"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:51:04.841425679"
+        "timestamp": "2025-04-11T15:38:00.970356064"
     },
     "genmod_models": {
         "content": [
             [
-                "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+                "versions.yml:md5,ea3c11abc1c5be5d8c0fd50ca4bb2344"
             ],
             "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:49:56.642318737"
+        "timestamp": "2025-04-11T15:37:48.695367113"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml
index 163ddf093118..38153d167024 100644
--- a/modules/nf-core/genmod/score/environment.yml
+++ b/modules/nf-core/genmod/score/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.9
+  - bioconda::genmod=3.10
diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf
index 756fc73132a3..bc3b8547d622 100644
--- a/modules/nf-core/genmod/score/main.nf
+++ b/modules/nf-core/genmod/score/main.nf
@@ -4,8 +4,8 @@ process GENMOD_SCORE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
-        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10--pyh7e72e81_0':
+        'biocontainers/genmod:3.10--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf), path (fam)
diff --git a/modules/nf-core/genmod/score/tests/main.nf.test.snap b/modules/nf-core/genmod/score/tests/main.nf.test.snap
index b484b8e12aed..2a6a7ec7922c 100644
--- a/modules/nf-core/genmod/score/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/score/tests/main.nf.test.snap
@@ -2,15 +2,15 @@
     "genmod_score": {
         "content": [
             [
-                "versions.yml:md5,f310225b3c35456e84d52e2c400e2fd8"
+                "versions.yml:md5,d9e6ac07d6f647bfefbdbe45fe094a2b"
             ],
             "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:50:12.03483811"
+        "timestamp": "2025-04-11T15:38:15.954815178"
     },
     "genmod_score - stub": {
         "content": [
@@ -25,7 +25,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,f310225b3c35456e84d52e2c400e2fd8"
+                    "versions.yml:md5,d9e6ac07d6f647bfefbdbe45fe094a2b"
                 ],
                 "vcf": [
                     [
@@ -37,14 +37,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f310225b3c35456e84d52e2c400e2fd8"
+                    "versions.yml:md5,d9e6ac07d6f647bfefbdbe45fe094a2b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-25T11:50:19.675962486"
+        "timestamp": "2025-04-11T15:38:33.518191239"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf
index c99ab826042b..0c2984fb503a 100644
--- a/modules/nf-core/genotyphi/parse/main.nf
+++ b/modules/nf-core/genotyphi/parse/main.nf
@@ -18,8 +18,9 @@ process GENOTYPHI_PARSE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
     parse_typhi_mykrobe.py \\
         --jsons $json \\
@@ -30,4 +31,15 @@ process GENOTYPHI_PARSE {
         genotyphi: \$(echo \$(genotyphi --version 2>&1) | sed 's/^.*GenoTyphi v//;' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.tsv
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genotyphi: \$(echo \$(genotyphi --version 2>&1) | sed 's/^.*GenoTyphi v//;' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/genotyphi/parse/tests/main.nf.test b/modules/nf-core/genotyphi/parse/tests/main.nf.test
new file mode 100644
index 000000000000..b6ba207342a0
--- /dev/null
+++ b/modules/nf-core/genotyphi/parse/tests/main.nf.test
@@ -0,0 +1,68 @@
+nextflow_process {
+
+    name "Test Process GENOTYPHI_PARSE"
+
+    script "../main.nf"
+    process "GENOTYPHI_PARSE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mykrobe"
+    tag "mykrobe/predict"
+    tag "genotyphi"
+    tag "genotyphi/parse"
+
+    setup {
+        run("MYKROBE_PREDICT") {
+            script "../../../mykrobe/predict/main.nf"
+            
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam',checkIfExists:true)
+                    ]
+                input[1] = "typhi"
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - json") {
+        when {
+            
+            process {
+                """
+                input[0] = MYKROBE_PREDICT.out.json
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - json -- stub") {
+        options "-stub"
+        when {
+            
+            process {
+                """
+                input[0] = MYKROBE_PREDICT.out.json
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genotyphi/parse/tests/main.nf.test.snap b/modules/nf-core/genotyphi/parse/tests/main.nf.test.snap
new file mode 100644
index 000000000000..c083a6990548
--- /dev/null
+++ b/modules/nf-core/genotyphi/parse/tests/main.nf.test.snap
@@ -0,0 +1,77 @@
+{
+    "sarscov2 - json": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_predictResults.tsv:md5,b13d2b83139d894245ad2f2a233d1029"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8832872a868b1270d21f6b93685b6eed"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_predictResults.tsv:md5,b13d2b83139d894245ad2f2a233d1029"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8832872a868b1270d21f6b93685b6eed"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-10T11:22:29.761275502"
+    },
+    "sarscov2 - json -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8832872a868b1270d21f6b93685b6eed"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8832872a868b1270d21f6b93685b6eed"
+                ]
+            },
+            {
+                "GENOTYPHI_PARSE": {
+                    "genotyphi": "1.9.1"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-10T11:22:35.524513078"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf
index 23862fee5739..c9ef29a58075 100644
--- a/modules/nf-core/gtdbtk/classifywf/main.nf
+++ b/modules/nf-core/gtdbtk/classifywf/main.nf
@@ -2,24 +2,24 @@ process GTDBTK_CLASSIFYWF {
     tag "${prefix}"
     label 'process_medium'
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' : 'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1'}"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_2' : 'biocontainers/gtdbtk:2.4.0--pyhdfd78af_2'}"
 
     input:
-    tuple val(meta)   , path("bins/*")
-    tuple val(db_name), path("database/*")
+    tuple val(meta), path("bins/*")
+    tuple val(db_name), path(db)
     val use_pplacer_scratch_dir
     path mash_db
 
     output:
-    tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv")        , emit: summary
-    tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz")   , emit: tree    , optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv"), emit: markers , optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz")       , emit: msa     , optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz")  , emit: user_msa, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv")       , emit: filtered, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv")   , emit: failed  , optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.log")                  , emit: log
-    tuple val(meta), path("gtdbtk.${prefix}.warnings.log")         , emit: warnings
+    tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv"), emit: summary
+    tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz"), emit: tree, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv"), emit: markers, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz"), emit: msa, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz"), emit: user_msa, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv"), emit: filtered, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv"), emit: failed, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.log"), emit: log
+    tuple val(meta), path("gtdbtk.${prefix}.warnings.log"), emit: warnings
     path ("versions.yml"), emit: versions
 
     when:
@@ -28,12 +28,13 @@ process GTDBTK_CLASSIFYWF {
     script:
     def args = task.ext.args ?: ''
     def pplacer_scratch = use_pplacer_scratch_dir ? "--scratch_dir pplacer_tmp" : ""
-    def mash_mode       = mash_db                 ? "--mash_db ${mash_db}"      : "--skip_ani_screen"
+    def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen"
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    export GTDBTK_DATA_PATH="\${PWD}/database"
-    if [ ${pplacer_scratch} != "" ] ; then
+    export GTDBTK_DATA_PATH="\$(find -L ${db} -name 'metadata' -type d -exec dirname {} \\;)"
+
+    if [ "${pplacer_scratch}" != "" ] ; then
         mkdir pplacer_tmp
     fi
 
@@ -68,7 +69,7 @@ process GTDBTK_CLASSIFYWF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
+        gtdbtk: \$(echo \$(gtdbtk --version 2>/dev/null) | sed "s/gtdbtk: version //; s/ Copyright.*//")
     END_VERSIONS
     """
 
@@ -87,7 +88,7 @@ process GTDBTK_CLASSIFYWF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
+        gtdbtk: \$(echo \$(gtdbtk --version 2>/dev/null) | sed "s/gtdbtk: version //; s/ Copyright.*//")
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/gtdbtk/classifywf/meta.yml b/modules/nf-core/gtdbtk/classifywf/meta.yml
index fc081897d80c..fc31a609fe24 100644
--- a/modules/nf-core/gtdbtk/classifywf/meta.yml
+++ b/modules/nf-core/gtdbtk/classifywf/meta.yml
@@ -27,13 +27,18 @@ input:
           e.g. [ id:'test', single_end:false,  assembler:'spades' ]
     - '"bins/*"':
         type: file
-        description: bins
+        description: A list of one or more bins in FASTA format for classification
+        pattern: "*.{fasta,fna,fas,fa}{,.gz}"
   - - db_name:
         type: string
         description: The name of the GTDB database to use.
-    - '"database/*"':
+    - db:
         type: file
-        description: GTDB database
+        description: |
+          Path to a directory containing a GDTB database, as uncompressed from from the 'full package' gtdbdtk_data.tar.gz file.
+          You can give the 'release<version number>' directory here.
+          Must contain the 'metadata' subdirectory
+        pattern: "release[0-9]+\/"
   - - use_pplacer_scratch_dir:
         type: boolean
         description: Set to true to reduce pplacer memory usage by writing to disk (slower)
diff --git a/modules/nf-core/integronfinder/environment.yml b/modules/nf-core/integronfinder/environment.yml
new file mode 100644
index 000000000000..c5ef37127842
--- /dev/null
+++ b/modules/nf-core/integronfinder/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::integron_finder=2.0.5=pyhdfd78af_0
diff --git a/modules/nf-core/integronfinder/main.nf b/modules/nf-core/integronfinder/main.nf
new file mode 100644
index 000000000000..ae6431c261df
--- /dev/null
+++ b/modules/nf-core/integronfinder/main.nf
@@ -0,0 +1,65 @@
+process INTEGRONFINDER {
+    tag "$meta.id"
+    label 'process_low'
+
+    containerOptions workflow.containerEngine == 'singularity' ? 
+        '--env MPLCONFIGDIR=/tmp/mplconfigdir' :
+        '-e MPLCONFIGDIR=/tmp/mplconfigdir'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/integron_finder:2.0.5--pyhdfd78af_0':
+        'biocontainers/integron_finder:2.0.5--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*/*.gbk")              , emit: gbk, optional: true
+    tuple val(meta), path("*/*.integrons")        , emit: integrons
+    tuple val(meta), path("*/*.summary")          , emit: summary
+    tuple val(meta), path("*/integron_finder.out"), emit: out
+    path "versions.yml"                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args                = task.ext.args ?: ''
+    def is_compressed_fasta = fasta.getName().endsWith(".gz") ? true : false
+    def fasta_name          = fasta.getName().replace(".gz", "")
+    
+    """
+    if [ "$is_compressed_fasta" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    integron_finder \\
+        $args \\
+        --cpu $task.cpus \\
+        $fasta_name
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        integronfinder: \$(integron_finder --version 2>&1 | head -n1 | sed 's/^integron_finder version //' | cut -d ' ' -f1)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def gbk_create = args.contains("--gbk") ? "Results_Integron_Finder_${prefix}/${prefix}.gbk" : ""
+
+    """
+    mkdir -p Results_Integron_Finder_${prefix}
+    ${gbk_create}
+    touch "Results_Integron_Finder_${prefix}/${prefix}.integrons"
+    touch "Results_Integron_Finder_${prefix}/${prefix}.summary"
+    touch "Results_Integron_Finder_${prefix}/integron_finder.out"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        integronfinder: \$(integron_finder --version 2>&1 | head -n1 | sed 's/^integron_finder version //' | cut -d ' ' -f1)
+    END_VERSIONS
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/integronfinder/meta.yml b/modules/nf-core/integronfinder/meta.yml
new file mode 100644
index 000000000000..fe18d4d7fbbc
--- /dev/null
+++ b/modules/nf-core/integronfinder/meta.yml
@@ -0,0 +1,86 @@
+name: integronfinder
+description: Detect integrons in DNA sequences
+keywords:
+  - bacteria
+  - fasta
+  - mobile genetic elements
+  - integron
+tools:
+  - integronfinder:
+      description: "Integron Finder aims at detecting independently integron integrase
+        and attC recombination sites in DNA sequences"
+      homepage: "https://integronfinder.readthedocs.io/en/latest/"
+      documentation: "https://integronfinder.readthedocs.io/en/latest/"
+      tool_dev_url: "https://github.com/gem-pasteur/Integron_Finder/"
+      doi: "10.3390/microorganisms10040700"
+      licence: ["GPL v3-or-later"]
+      identifier: biotools:integron_finder
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Nucleotide sequences in FASTA format
+        pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/data_2977" # Nucleic acid sequence
+          - edam: "http://edamontology.org/format_1929" #FASTA
+output:
+  - gbk:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*/*.gbk":
+          type: file
+          description: Creates a Genbank files with all the annotations found (present in the .integrons file)
+          pattern: "*.gbk"
+          ontologies: &id001
+            - edam: "http://edamontology.org/format_1936" # GenBank
+  - integrons:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*/*.integrons":
+          type: file
+          description: A file with all integrons and their elements detected in all sequences in the input file
+          pattern: "*.integrons"
+  - summary:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*/*.summary":
+          type: file
+          description: A summary file with the number and type of integrons per sequence
+          pattern: "*.summary"
+  - out:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*/integron_finder.out":
+          type: file
+          description: A copy standard output. The stdout can be silenced with the argument --mute
+          pattern: "integron_finder.out"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@nguyent-son"
+  - "@juke34"
+  - "@jhayer"
+maintainers:
+  - "@nguyent-son"
+  - "@juke34"
+  - "@jhayer"
diff --git a/modules/nf-core/integronfinder/tests/main.nf.test b/modules/nf-core/integronfinder/tests/main.nf.test
new file mode 100644
index 000000000000..dff2b779abd0
--- /dev/null
+++ b/modules/nf-core/integronfinder/tests/main.nf.test
@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process INTEGRONFINDER"
+    script "../main.nf"
+    process "INTEGRONFINDER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "integronfinder"
+
+    test("IntegronFinder - escherichia_coli - genome_fa_gz") {
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.out[0][1]).readLines().get(56).contains("command used: integron_finder") },
+                { assert snapshot(
+                        process.out.gbk ? path(process.out.gbk[0][1]).text : "no_gbk",
+                        path(process.out.summary[0][1]).readLines()[1..-1], // Remove first line due to hash presence in conda
+                        path(process.out.integrons[0][1]).readLines()[1..-1],
+                        process.out.versions,
+                        path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("IntegronFinder - escherichia_coli - genome_fa_gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/integronfinder/tests/main.nf.test.snap b/modules/nf-core/integronfinder/tests/main.nf.test.snap
new file mode 100644
index 000000000000..19610d53ba31
--- /dev/null
+++ b/modules/nf-core/integronfinder/tests/main.nf.test.snap
@@ -0,0 +1,106 @@
+{
+    "IntegronFinder - escherichia_coli - genome_fa_gz": {
+        "content": [
+            "no_gbk",
+            [
+                "# cmd: integron_finder --cpu 2 genome.fa",
+                "ID_replicon\tCALIN\tcomplete\tIn0\ttopology\tsize",
+                "chr\t0\t0\t0\tcirc\t48502"
+            ],
+            [
+                "# cmd: integron_finder --cpu 2 genome.fa",
+                "# No Integron found"
+            ],
+            [
+                "versions.yml:md5,381190cf27737ed39ada1dfeec09dbe8"
+            ],
+            {
+                "INTEGRONFINDER": {
+                    "integronfinder": "2.0.5"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-02T18:53:05.832325584"
+    },
+    "IntegronFinder - escherichia_coli - genome_fa_gz - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.integrons:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "integron_finder.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,381190cf27737ed39ada1dfeec09dbe8"
+                ],
+                "gbk": [
+                    
+                ],
+                "integrons": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.integrons:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "integron_finder.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,381190cf27737ed39ada1dfeec09dbe8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-02T16:19:41.207197789"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/limma/differential/tests/main.nf.test b/modules/nf-core/limma/differential/tests/main.nf.test
index 4cdd0014e716..551a53f12d7a 100644
--- a/modules/nf-core/limma/differential/tests/main.nf.test
+++ b/modules/nf-core/limma/differential/tests/main.nf.test
@@ -220,7 +220,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(process.out.model, process.out.versions).match() },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-4.89014922224241") },
-                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.779227180297504") },
+                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.77922") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
             )
@@ -249,7 +249,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(process.out.model, process.out.versions).match() },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.84055986312942") },
-                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.705508451587681") },
+                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7055") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
             )
@@ -278,7 +278,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(process.out.model, process.out.versions).match() },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.8363444336503") },
-                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.736009837885068") },
+                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7360") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
             )
diff --git a/modules/nf-core/links/environment.yml b/modules/nf-core/links/environment.yml
new file mode 100644
index 000000000000..9b3fd0b63736
--- /dev/null
+++ b/modules/nf-core/links/environment.yml
@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::links=2.0.1"
diff --git a/modules/nf-core/links/main.nf b/modules/nf-core/links/main.nf
new file mode 100644
index 000000000000..c55bc661e270
--- /dev/null
+++ b/modules/nf-core/links/main.nf
@@ -0,0 +1,85 @@
+process LINKS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/links:2.0.1--h4ac6f70_5':
+        'biocontainers/links:2.0.1--h4ac6f70_5' }"
+
+    input:
+    tuple val(meta), path(assembly)
+    tuple val(meta2), path(reads)
+
+    output:
+    tuple val(meta), path("*.log"),                         emit: log
+    tuple val(meta), path("*.pairing_distribution.csv"),    emit: pairing_distribution,  optional: true
+    tuple val(meta), path("*.pairing_issues"),              emit: pairing_issues
+    tuple val(meta), path("*.scaffolds"),                   emit: scaffolds_csv
+    tuple val(meta), path("*.scaffolds.fa"),                emit: scaffolds_fasta
+    tuple val(meta), path("*.bloom"),                       emit: bloom
+    tuple val(meta), path("*.gv"),                          emit: scaffolds_graph
+    tuple val(meta), path("*.assembly_correspondence.tsv"), emit: assembly_correspondence
+    tuple val(meta), path("*.simplepair_checkpoint.tsv"),   emit: simplepair_checkpoint, optional: true
+    tuple val(meta), path("*.tigpair_checkpoint.tsv"),      emit: tigpair_checkpoint
+    path "versions.yml",                                    emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Currently LINKS does not support more than 4 threads
+    def nthreads = "${task.cpus}" < 4 ? "${task.cpus}" : 4
+    def args = task.ext.args ?: ""
+    """
+    if [[ ${assembly} == *.gz ]];
+    then
+        gzip -dc ${assembly} > assembly.fa
+    else
+        ln -s ${assembly} assembly.fa
+    fi
+
+    for read_file in ${reads};
+        do
+            if [[ \$read_file == *.gz ]];
+            then 
+                gzip -dc \$read_file > \$(basename \$read_file .gz)
+                echo \$(basename \$read_file .gz) >> readfile.fof
+            else
+                echo \$read_file >> readfile.fof
+            fi
+        done
+
+    LINKS -f assembly.fa \\
+        -s readfile.fof \\
+        -j $nthreads \\
+        -b ${prefix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        LINKS: \$(echo \$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//'))
+    END_VERSIONS
+    """
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.log
+    touch ${prefix}.pairing_distribution.csv
+    touch ${prefix}.pairing_issues
+    touch ${prefix}.scaffolds
+    touch ${prefix}.scaffolds.fa
+    touch ${prefix}.bloom
+    touch ${prefix}.gv
+    touch ${prefix}.assembly_correspondence.tsv
+    touch ${prefix}.simplepair_checkpoint.tsv
+    touch ${prefix}.tigpair_checkpoint.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        LINKS: \$(echo \$(LINKS | grep -o 'LINKS v.*' | sed 's/LINKS v//'))
+    END_VERSIONS
+    """
+    }
diff --git a/modules/nf-core/links/meta.yml b/modules/nf-core/links/meta.yml
new file mode 100644
index 000000000000..94004cdc2167
--- /dev/null
+++ b/modules/nf-core/links/meta.yml
@@ -0,0 +1,175 @@
+---
+name: "links"
+description: | 
+      LINKS is a genomics application for scaffolding genome assemblies with long reads,
+      such as those produced by Oxford Nanopore Technologies Ltd. 
+      It can be used to scaffold high-quality draft genome assemblies with any long sequences 
+      (eg. ONT reads, PacBio reads, other draft genomes, etc). 
+      It is also used to scaffold contig pairs linked by ARCS/ARKS.
+      This module is for LINKS >=2.0.0 and does not support MPET input.
+keywords:
+  - scaffold
+  - long-reads
+  - genomics
+tools:
+  - "links":
+      description: "Long Interval Nucleotide K-mer Scaffolder"
+      homepage: "https://www.bcgsc.ca/resources/software/links"
+      documentation: "https://github.com/bcgsc/LINKS"
+      tool_dev_url: "https://github.com/bcgsc/LINKS"
+      doi: "10.1186/s13742-015-0076-3"
+      licence: ['GPL v3']
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - assembly:
+        type: file
+        description: (Multi-)fasta file containing the draft assembly
+        pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - reads:
+        type: file
+        description: fastq file(s) containing the long reads to be used for scaffolding
+        pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+
+output:
+  - log:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.log":
+        type: file
+        description: text file; Logs execution time / errors / pairing stats.
+        pattern: "*.log"
+  - pairing_distribution:
+     - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+     - "*.pairing_distribution.csv":
+        type: file
+        description: |
+          comma-separated file; 1st column is the calculated distance
+          for each pair (template) with reads that assembled logically
+          within the same contig. 2nd column is the number of pairs at
+          that distance.
+        pattern: "*.pairing_distribution.csv"
+  - pairing_issues:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`  
+    - "*.pairing_issues":
+        type: file
+        description: |
+          text file; Lists all pairing issues encountered between contig
+          pairs and illogical/out-of-bounds pairing.
+        pattern: "*.pairing_issues"
+  - scaffolds_csv:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.scaffolds":
+        type: file
+        description: comma-separated file; containing the new scaffold(s)
+        pattern: "*.scaffolds"
+  - scaffolds_fasta:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.scaffolds.fa":
+        type: file
+        description: fasta file of the new scaffold sequence
+        pattern: "*.scaffolds.fa"
+  - bloom:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.bloom":
+        type: file
+        description: | 
+          Bloom filter created by shredding the -f input
+          into k-mers of size -k
+        pattern: "*.bloom"
+  - scaffolds_graph:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.gv":
+        type: file
+        description: | 
+          scaffold graph (for visualizing merges), can be rendered 
+          in neato, graphviz, etc
+        pattern: "*.gv"
+  - assembly_correspondence:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.assembly_correspondence.tsv":
+        type: file
+        description: |
+          correspondence file lists the scaffold ID,
+          contig ID, original_name, #linking kmer pairs,
+          links ratio, gap or overlap
+        pattern: "*.assembly_correspondence.tsv"
+  - simplepair_checkpoint:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.simplepair_checkpoint.tsv":
+        type: file
+        description: checkpoint file, contains info to rebuild datastructure for .gv graph
+        pattern: "*.simplepair_checkpoint.tsv"
+  - tigpair_checkpoint:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1']`
+    - "*.tigpair_checkpoint.tsv":
+        type: file
+        description: |
+          if -b BASNAME.tigpair_checkpoint.tsv is present, 
+          LINKS will skip the kmer pair extraction and contig pairing stages.
+          Delete this file to force LINKS to start at the beginning.
+          This file can be used to: 
+          1) quickly test parameters (-l min. links / -a min. links ratio), 
+          2) quickly recover from crash,
+          3) explore very large kmer spaces,
+          4) scaffold with output of ARCS
+        pattern: "*.tigpair_checkpoint.tsv"
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@nschan"
+maintainers:
+  - "@nschan"
diff --git a/modules/nf-core/links/tests/main.nf.test b/modules/nf-core/links/tests/main.nf.test
new file mode 100644
index 000000000000..4b449ab27eb2
--- /dev/null
+++ b/modules/nf-core/links/tests/main.nf.test
@@ -0,0 +1,163 @@
+nextflow_process {
+    name "Test Process LINKS"
+    script "../main.nf"
+    process "LINKS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "links"
+
+    test("LINKS - LINKS test data") {
+        config './nextflow.config'
+
+        when {
+            params {
+                module_args = "-d 1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,12000,14000,16000,18000,20000"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/contigs.fasta', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'test'], 
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/genome.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    process.out.pairing_issues,
+                    process.out.scaffolds_csv,
+                    process.out.scaffolds_fasta,
+                    process.out.bloom,
+                    file(process.out.scaffolds_graph[0][1]).name,
+                    process.out.assembly_correspondence,
+                    process.out.tigpair_checkpoint,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("LINKS - longstitch test data 1") {
+        config './nextflow.config'
+
+        when {
+            params {
+                module_args = "-d 1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,12000,14000,16000,18000,20000"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_scaffolds1.fa', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'test'], 
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_reads1.fa.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    file(process.out.pairing_issues[0][1]).name,
+                    process.out.scaffolds_csv,
+                    process.out.scaffolds_fasta,
+                    process.out.bloom,
+                    file(process.out.scaffolds_graph[0][1]).name,
+                    file(process.out.assembly_correspondence[0][1]).name,
+                    file(process.out.tigpair_checkpoint[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+    test("LINKS - longstitch test data 2") {
+        config './nextflow.config'
+
+        when {
+            params {
+                module_args = "-d 1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,12000,14000,16000,18000,20000"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_scaffolds2.fa', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'test'], 
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_reads2.fa.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    file(process.out.pairing_issues[0][1]).name,
+                    process.out.scaffolds_csv,
+                    process.out.scaffolds_fasta,
+                    process.out.bloom,
+                    file(process.out.scaffolds_graph[0][1]).name,
+                    file(process.out.assembly_correspondence[0][1]).name,
+                    file(process.out.tigpair_checkpoint[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+    test("LINKS - stub") {
+
+        options "-stub"
+        config './nextflow.config'
+
+        when {
+            params {
+                module_args = "-d 1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,12000,14000,16000,18000,20000"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], 
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/contigs.fasta', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'test' ], 
+                    file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/genome.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/links/tests/main.nf.test.snap b/modules/nf-core/links/tests/main.nf.test.snap
new file mode 100644
index 000000000000..0e2507a3824a
--- /dev/null
+++ b/modules/nf-core/links/tests/main.nf.test.snap
@@ -0,0 +1,323 @@
+{
+    "LINKS - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pairing_distribution.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    "versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pairing_issues:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scaffolds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scaffolds.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bloom:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.assembly_correspondence.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.simplepair_checkpoint.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tigpair_checkpoint.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "assembly_correspondence": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.assembly_correspondence.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bloom": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bloom:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pairing_distribution": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pairing_distribution.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pairing_issues": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pairing_issues:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "scaffolds_csv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scaffolds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "scaffolds_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scaffolds.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "scaffolds_graph": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "simplepair_checkpoint": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.simplepair_checkpoint.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tigpair_checkpoint": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tigpair_checkpoint.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-11T11:49:53.947870525"
+    },
+    "LINKS - longstitch test data 1": {
+        "content": [
+            "test.log",
+            "test.pairing_issues",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.scaffolds:md5,e12db5e5e6a1b5e26d2b50b6256c960d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.scaffolds.fa:md5,afe56607a3d2c3b1e2d605bdf7ca545f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bloom:md5,b912b31cfadaf81e722f5441ac639f60"
+                ]
+            ],
+            "test.gv",
+            "test.assembly_correspondence.tsv",
+            "test.tigpair_checkpoint.tsv",
+            [
+                "versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-11T13:39:00.252899964"
+    },
+    "LINKS - longstitch test data 2": {
+        "content": [
+            "test.log",
+            "test.pairing_issues",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.scaffolds:md5,00a943691b987adebe0ab40efced9c7e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.scaffolds.fa:md5,ed43c629e8d440e3cf6fb8b21742557c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bloom:md5,695262bb4beda52665d2f7ec476a4e7b"
+                ]
+            ],
+            "test.gv",
+            "test.assembly_correspondence.tsv",
+            "test.tigpair_checkpoint.tsv",
+            [
+                "versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-11T13:39:36.483298325"
+    },
+    "LINKS - LINKS test data": {
+        "content": [
+            "test.log",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.pairing_issues:md5,eb8b04b4ec170a319b40d2ee16a5cf96"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.scaffolds:md5,afe5339405b830e97095058080550064"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.scaffolds.fa:md5,4aa442ee4b05e1608daf7b5b033a4203"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bloom:md5,96f54f577d1c589251ea0cfe624b898d"
+                ]
+            ],
+            "test.gv",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.assembly_correspondence.tsv:md5,0efc40db474ba8d5b334ad48add4bd9d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.tigpair_checkpoint.tsv:md5,9208c8fe686b5989eaec1485a74cf44e"
+                ]
+            ],
+            [
+                "versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-11T11:30:01.790074303"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/links/tests/nextflow.config b/modules/nf-core/links/tests/nextflow.config
new file mode 100644
index 000000000000..1279535c158f
--- /dev/null
+++ b/modules/nf-core/links/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'LINKS' {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/metaspace/download/environment.yml b/modules/nf-core/metaspace/download/environment.yml
new file mode 100644
index 000000000000..0dda43c69c33
--- /dev/null
+++ b/modules/nf-core/metaspace/download/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::metaspace2020=2.0.9
+  - conda-forge::pandas=2.2.3
+  - conda-forge::python=3.11.11
diff --git a/modules/nf-core/metaspace/download/main.nf b/modules/nf-core/metaspace/download/main.nf
new file mode 100644
index 000000000000..aa56a6133b70
--- /dev/null
+++ b/modules/nf-core/metaspace/download/main.nf
@@ -0,0 +1,42 @@
+process METASPACE_DOWNLOAD {
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c3/c317f9380b8b631acacad83ab362b2badb42e8782f6bfa03e5befe59f2382283/data':
+        'community.wave.seqera.io/library/python_pip_metaspace-converter:958b8906de66e072' }"
+
+    input:
+    tuple val(dataset_id), val(database), val(version)
+
+    output:
+    path "${dataset_id}_*.csv", optional: true, emit: results
+    stdout                                      emit: log  // check meta.yml for see how to use!
+    path 'versions.yml'                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'metaspace_download.py'
+
+    stub:
+    """
+    if [[ "${database}" != "null" && "${version}" != "null" ]]; then
+        touch ${dataset_id}_${database}_${version}.csv
+    elif [[ "${database}" != "null" ]]; then
+        touch ${dataset_id}_${database}_all_versions.csv
+    else
+        touch ${dataset_id}_all_databases.csv
+    fi
+
+    echo "Stub: Processing dataset_id: ${dataset_id}, database: ${database}, version: ${version}" > ${dataset_id}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        pandas: \$(python -c "import pandas; print(pandas.__version__)")
+        metaspace: \$(python -c "import metaspace; print(metaspace.__version__)")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/metaspace/download/meta.yml b/modules/nf-core/metaspace/download/meta.yml
new file mode 100644
index 000000000000..b31e14764f74
--- /dev/null
+++ b/modules/nf-core/metaspace/download/meta.yml
@@ -0,0 +1,78 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "metaspace_download"
+description: A module to download dataset results from the METASPACE platform and
+  save them as CSV files, using a containerized Python script. Inputs are provided
+  via a CSV file or a list of datasets, with results saved to a specified output directory.
+keywords:
+  - metaspace
+  - metabolite annotation
+  - data-download
+  - csv
+tools:
+  - metaspace2020:
+      description: Python package providing programmatic access to the METASPACE platform
+      homepage: https://metaspace2020.readthedocs.io
+      documentation: https://metaspace2020.readthedocs.io
+      tool_dev_url: https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client
+      licence: ["Apache-2.0 license"]
+input:
+  - - dataset_id:
+        type: string
+        description: |
+          The ID of the dataset to process.
+          The ID is the last part of the dataset URL.
+          For example, in the URL `https://metaspace2020.org/dataset/2022-08-05_17h28m56s`,
+          the `dataset_id` is `2022-08-05_17h28m56s`.
+        optional: false
+    - database:
+        type: string
+        description: |
+          The database to download the dataset from (default: 'HMDB').
+          If not provided, all dataset will be included.
+        optional: true
+    - version:
+        type: string
+        description: |
+          The version of the database to download the dataset from (default: 'v4').
+          If not provided, all versions will be included.
+        optional: true
+
+output:
+  - results:
+      - ${dataset_id}_*.csv:
+          type: file
+          description: |
+            CSV file containing the downloaded dataset results, saved to the directory specified by the output parameter.
+            Filename format is '{dataset_id}_*.csv'.
+          pattern: "*.csv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3752:latest" # CSV format
+  - log:
+      - "emit:":
+          type: string
+          description: |
+            The standard output (stdout) of the script, containing log messages.
+            You can print the last log to see the download progress of all the datasets.
+            Example:
+              METASPACE_DOWNLOAD.out.log.view { "${it.split('\n').last().trim()}" }
+            It will print the last log message of the script.
+            For Example:
+              "❌ {dataset_id} Dataset not found or inaccessible. Skipping this dataset."
+              "❌ {dataset_id} could not find database: {database}"
+              "❌ {dataset_id} has no annotation data in database: {database}."
+              "⚠️ {dataset_id} has multiple {database} version. All the version saved to {filename}"
+              "✅ {dataset_id} with {database} database are saved to {filename}"
+              "✅ {dataset_id} with all database are saved to {filename}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: |
+            YAML file containing the versions of the tools used in the pipeline.
+            This file is automatically generated by the pipeline and should not be modified.
+          pattern: "versions.yml"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475" # YAML format
+authors:
+  - "@Dewey-Wang"
+maintainers:
+  - "@Dewey-Wang"
diff --git a/modules/nf-core/metaspace/download/templates/metaspace_download.py b/modules/nf-core/metaspace/download/templates/metaspace_download.py
new file mode 100644
index 000000000000..6da11dc1bffd
--- /dev/null
+++ b/modules/nf-core/metaspace/download/templates/metaspace_download.py
@@ -0,0 +1,161 @@
+#!/usr/bin/env python3
+
+import platform
+
+import metaspace
+import pandas as pd
+from metaspace import SMInstance
+
+
+def download_dataset_results(dataset_id, database=None, version=None):
+    """
+    Download the results of a specified dataset and save them as a CSV file.
+
+    Args:
+        dataset_id (str): The ID of the dataset to process.
+            The ID is the last part of the dataset URL.
+            For example, in the URL `https://metaspace2020.org/dataset/2022-08-05_17h28m56s`,
+            the `dataset_id` is `2022-08-05_17h28m56s`.
+        database (str, optional): The name of the database to filter. If not provided, all databases will be included.
+        version (str, optional): The version of the database to filter. If not provided, all versions will be included.
+
+    Returns:
+        pd.DataFrame: A DataFrame containing the results.
+
+    Behavior:
+        - If only `database` is provided and it has multiple versions, the results will be combined into one file named `{database}_all_versions.csv`.
+        - If the `database` has only one version, the file will be named `{database}_{version}.csv`.
+        - If no `database` is provided, it will download all the annotations file from all database and the file will be named `all_databases.csv`.
+    """
+    # Retrieve the dataset object
+    print(f"Processing dataset_id: {dataset_id}, database: {database}, version: {version}")
+    # print("Initializing SMInstance...")
+    sm = SMInstance()
+    print(f"Fetching dataset: {dataset_id}")
+    try:
+        dataset = sm.dataset(id=dataset_id)
+    except Exception:
+        print(f"❌ {dataset_id} Dataset not found or inaccessible. Skipping this dataset.")
+        return None
+
+    # Step 1: Generate annotation statistics table
+    # print("Fetching database details...")
+    databases = dataset.database_details
+    # Extract database names and versions
+    database_info = []
+    for db in databases:
+        db_str = str(db)
+        name_version = db_str.split(":")[1:3]
+        name_version = [nv.strip(">") for nv in name_version]  # Remove trailing '>'
+        database_info.append(" ".join(name_version))
+
+    print("Available databases and versions:")
+    for db in database_info:
+        print(f"  - {db}")
+
+    # Check if the multiple versions database exists
+    has_multiple_versions = False
+    # Check if the specified database exists
+    if database:
+        matched_databases = [db for db in database_info if db.startswith(database)]
+        if not matched_databases:
+            print(f"❌ {dataset_id} could not find database: {database}")
+            return None
+        elif len(matched_databases) > 1 and version is None:
+            has_multiple_versions = True
+            print(f"Warning: Multiple versions found for database {database}.")
+            print("Available versions:")
+            for db in matched_databases:
+                print(f"  - {db}")
+
+    # Initialize the results DataFrame
+    results_df = pd.DataFrame()
+
+    # Process the specified database names and versions
+    for db in database_info:
+        name, ver = db.split()
+        if (database is None or database == name) and (version is None or version == ver):
+            print(f"Processing database: {name}, version: {ver}")
+            result = dataset.results(database=(name, ver))
+            result_df = pd.DataFrame(result)
+            result_df["Database"] = name
+            result_df["Version"] = ver
+            results_df = pd.concat([results_df, result_df], ignore_index=True)
+
+    if results_df.empty:
+        print(f"❌ {dataset_id} has no annotation data in database: {database}.")
+        return None
+
+    # Extract the content of '+adduct' and '-adduct''
+    if "ion" in results_df.columns:
+        results_df["Adduct"] = results_df["ion"].str.extract(r"([+-][A-Za-z0-9]+)")
+    # Rename the `intensity` column to `maxIntensity`
+    if "intensity" in results_df.columns:
+        results_df.rename(columns={"intensity": "maxIntensity"}, inplace=True)
+
+    # Dynamically generate the CSV file name
+    if database:
+        matched_versions = [db.split()[1] for db in database_info if db.startswith(database)]
+        if len(matched_versions) > 1:
+            filename = f"{dataset_id}_{database}_all_versions.csv"
+        else:
+            filename = f"{dataset_id}_{database}_{matched_versions[0]}.csv"
+    else:
+        filename = f"{dataset_id}_all_databases.csv"
+
+    # Save the results to a CSV file
+    results_df.to_csv(filename, index=False)
+    if has_multiple_versions:
+        print(f"⚠️ {dataset_id} has multiple {database} version. All the version saved to {filename}")
+    elif database:
+        print(f"✅ {dataset_id} with {database} database are saved to {filename}")
+    else:
+        print(f"✅ {dataset_id} with all database are saved to {filename}")
+
+    return results_df
+
+
+dataset_id = "${dataset_id}"
+
+if dataset_id == "null" or dataset_id is None:
+    raise ValueError("Error: input csv or datasets contains an entry with missing dataset_id.")
+
+database = "${database}" if "${database}" != "null" else None
+version = "${version}" if "${version}" != "null" else None
+
+result = download_dataset_results(dataset_id, database, version)
+
+
+def format_yaml_like(data: dict, indent: int = 0) -> str:
+    """Formats a dictionary to a YAML-like string.
+
+    Args:
+        data (dict): The dictionary to format.
+        indent (int): The current indentation level.
+
+    Returns:
+        str: A string formatted as YAML.
+    """
+    yaml_str = ""
+    for key, value in data.items():
+        spaces = "    " * indent
+        if isinstance(value, dict):
+            yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}"
+        else:
+            yaml_str += f"{spaces}{key}: {value}\\n"
+    return yaml_str
+
+
+# Versions
+
+versions = {
+    "${task.process}": {
+        "python": platform.python_version(),
+        "pandas": pd.__version__,
+        "metaspace": metaspace.__version__,
+    }
+}
+
+with open("versions.yml", "w") as f:
+    f.write(format_yaml_like(versions))
+print("versions.yml file has been generated.")
diff --git a/modules/nf-core/metaspace/download/tests/main.nf.test b/modules/nf-core/metaspace/download/tests/main.nf.test
new file mode 100644
index 000000000000..cf1b78cd32d5
--- /dev/null
+++ b/modules/nf-core/metaspace/download/tests/main.nf.test
@@ -0,0 +1,82 @@
+// nf-core modules test metaspace/download
+nextflow_process {
+
+    name "Test Process metaspace/download"
+    script "../main.nf"
+    process "METASPACE_DOWNLOAD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "metaspace"
+    tag "metaspace/download"
+
+    test("metaspace/download - datasets") {
+        when {
+            process {
+                """
+                input[0] = Channel.from([
+                    ['2022-08-05_17h28m56s', 'KEGG', null],
+                    ['2022-08-05_17h28m56s', null, null]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("metaspace/download - wrong_format") {
+        when {
+            process {
+                """
+                input[0] = Channel.from([
+                    ['2022-08-05_17h28m56s', 'KEGG', null],
+                    ['2022-08-05_17h28m56s', null, null],
+                    [null, 'KEGG', null] // Missing dataset_id
+                ])
+                """
+            }
+        }
+        then {
+            assert process.failed
+            assert process.exitStatus == 1
+
+            def errorMessage = process.stderr.find { it.contains("ValueError") } ?:
+                            process.stdout.find { it.contains("ValueError") }
+
+            println "Error message: ${errorMessage}"
+
+            assertAll(
+                { assert process.failed },
+                { assert process.exitStatus == 1 },
+                { assert errorMessage != null },
+                { assert errorMessage.contains("Error: input csv or datasets contains an entry with missing dataset_id") },
+                { assert snapshot(errorMessage).match("error_message") }
+            )
+        }
+    }
+    test("metaspace/download - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.from([
+                    ['2022-08-05_17h28m56s', 'KEGG', null],
+                    ['2022-08-05_17h28m56s', null, null]
+                ])
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/metaspace/download/tests/main.nf.test.snap b/modules/nf-core/metaspace/download/tests/main.nf.test.snap
new file mode 100644
index 000000000000..b394da34cc03
--- /dev/null
+++ b/modules/nf-core/metaspace/download/tests/main.nf.test.snap
@@ -0,0 +1,82 @@
+{
+    "error_message": {
+        "content": [
+            "      raise ValueError(\"Error: input csv or datasets contains an entry with missing dataset_id.\")"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-27T23:59:56.527423"
+    },
+    "metaspace/download - datasets": {
+        "content": [
+            {
+                "0": [
+                    "2022-08-05_17h28m56s_KEGG_v1.csv:md5,44a3760625f0e2f9aeee5639bd973d9b",
+                    "2022-08-05_17h28m56s_all_databases.csv:md5,93496262735b9f316f82c843c773a944"
+                ],
+                "1": [
+                    "Processing dataset_id: 2022-08-05_17h28m56s, database: KEGG, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: KEGG, version: v1\n\u2705 2022-08-05_17h28m56s with KEGG database are saved to 2022-08-05_17h28m56s_KEGG_v1.csv\nversions.yml file has been generated.\n",
+                    "Processing dataset_id: 2022-08-05_17h28m56s, database: None, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: HMDB-cotton, version: v4\nProcessing database: LipidMaps, version: 2017-12-12\nProcessing database: KEGG, version: v1\nProcessing database: BraChemDB, version: 2018-01\n\u2705 2022-08-05_17h28m56s with all database are saved to 2022-08-05_17h28m56s_all_databases.csv\nversions.yml file has been generated.\n"
+                ],
+                "2": [
+                    "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89",
+                    "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89"
+                ],
+                "log": [
+                    "Processing dataset_id: 2022-08-05_17h28m56s, database: KEGG, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: KEGG, version: v1\n\u2705 2022-08-05_17h28m56s with KEGG database are saved to 2022-08-05_17h28m56s_KEGG_v1.csv\nversions.yml file has been generated.\n",
+                    "Processing dataset_id: 2022-08-05_17h28m56s, database: None, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: HMDB-cotton, version: v4\nProcessing database: LipidMaps, version: 2017-12-12\nProcessing database: KEGG, version: v1\nProcessing database: BraChemDB, version: 2018-01\n\u2705 2022-08-05_17h28m56s with all database are saved to 2022-08-05_17h28m56s_all_databases.csv\nversions.yml file has been generated.\n"
+                ],
+                "results": [
+                    "2022-08-05_17h28m56s_KEGG_v1.csv:md5,44a3760625f0e2f9aeee5639bd973d9b",
+                    "2022-08-05_17h28m56s_all_databases.csv:md5,93496262735b9f316f82c843c773a944"
+                ],
+                "versions": [
+                    "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89",
+                    "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-05T14:05:56.321679"
+    },
+    "metaspace/download - stub": {
+        "content": [
+            {
+                "0": [
+                    "2022-08-05_17h28m56s_KEGG_all_versions.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "2022-08-05_17h28m56s_all_databases.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "",
+                    ""
+                ],
+                "2": [
+                    "versions.yml:md5,83b3435f6de10ae175f191530d4389dd",
+                    "versions.yml:md5,83b3435f6de10ae175f191530d4389dd"
+                ],
+                "log": [
+                    "",
+                    ""
+                ],
+                "results": [
+                    "2022-08-05_17h28m56s_KEGG_all_versions.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                    "2022-08-05_17h28m56s_all_databases.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,83b3435f6de10ae175f191530d4389dd",
+                    "versions.yml:md5,83b3435f6de10ae175f191530d4389dd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-05T14:15:24.315874"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/mindagap/duplicatefinder/environment.yml b/modules/nf-core/mindagap/duplicatefinder/environment.yml
index f9b2a1ac7520..5f748da68f34 100644
--- a/modules/nf-core/mindagap/duplicatefinder/environment.yml
+++ b/modules/nf-core/mindagap/duplicatefinder/environment.yml
@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - conda-forge::numpy=1.24.2
   - bioconda::mindagap=0.0.2
diff --git a/modules/nf-core/mindagap/duplicatefinder/main.nf b/modules/nf-core/mindagap/duplicatefinder/main.nf
index ad7ce5b238d2..794de7fdd6ad 100644
--- a/modules/nf-core/mindagap/duplicatefinder/main.nf
+++ b/modules/nf-core/mindagap/duplicatefinder/main.nf
@@ -2,9 +2,9 @@ process MINDAGAP_DUPLICATEFINDER {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::mindagap=0.0.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mindagap:0.0.2--pyhdfd78af_1':
+        'https://depot.galaxyproject.org/singularity/mindagap:0.0.2--pyhdfd78af_1' :
         'biocontainers/mindagap:0.0.2--pyhdfd78af_1' }"
 
     input:
@@ -18,8 +18,7 @@ process MINDAGAP_DUPLICATEFINDER {
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
     """
     duplicate_finder.py \\
         $spot_table \\
@@ -30,4 +29,14 @@ process MINDAGAP_DUPLICATEFINDER {
         mindagap: \$(mindagap.py test -v)
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${spot_table.baseName}_markedDups.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mindagap: \$(mindagap.py test -v)
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test b/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test
index d43a7de8358c..7e07f7412cb8 100644
--- a/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test
+++ b/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test
@@ -9,14 +9,46 @@ nextflow_process {
     tag "mindagap"
     tag "mindagap/duplicatefinder"
 
-    test("test_mindagap_duplicatefinder_spots") {
+    test("mindagap - duplicatefinder - spots - txt") {
 
         when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/molkart/'
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'test_data/input_data/spots.txt', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("mindagap - duplicatefinder - spots - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/molkart/'
+            }
+
             process {
                 """
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file('https://raw.githubusercontent.com/nf-core/test-datasets/molkart/test_data/input_data/spots.txt')
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'test_data/input_data/spots.txt', checkIfExists: true)
                     ]
                 """
             }
diff --git a/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test.snap b/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test.snap
index a1af5c2b905e..c43aee396617 100644
--- a/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test.snap
+++ b/modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test.snap
@@ -1,5 +1,38 @@
 {
-    "test_mindagap_duplicatefinder_spots": {
+    "mindagap - duplicatefinder - spots - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "spots_markedDups.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ae112b853ec32ee1c5eecaf421d01003"
+                ],
+                "marked_dups_spots": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "spots_markedDups.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ae112b853ec32ee1c5eecaf421d01003"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-02T19:57:30.980911113"
+    },
+    "mindagap - duplicatefinder - spots - txt": {
         "content": [
             {
                 "0": [
@@ -26,6 +59,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-11-30T22:56:20.101101751"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-02T19:57:24.039800026"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/mindagap/mindagap/main.nf b/modules/nf-core/mindagap/mindagap/main.nf
index 3f06996b5d0b..e738b27c0f5a 100644
--- a/modules/nf-core/mindagap/mindagap/main.nf
+++ b/modules/nf-core/mindagap/mindagap/main.nf
@@ -4,8 +4,8 @@ process MINDAGAP_MINDAGAP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/mindagap:0.0.2--pyhdfd78af_1' :
-    'biocontainers/mindagap:0.0.2--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/mindagap:0.0.2--pyhdfd78af_1' :
+        'biocontainers/mindagap:0.0.2--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(panorama)
@@ -18,8 +18,7 @@ process MINDAGAP_MINDAGAP {
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
     """
     mindagap.py \\
         $panorama \\
@@ -32,7 +31,6 @@ process MINDAGAP_MINDAGAP {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${panorama.baseName}_gridfilled.tiff
 
diff --git a/modules/nf-core/mindagap/mindagap/tests/main.nf.test b/modules/nf-core/mindagap/mindagap/tests/main.nf.test
index dbad49101be8..ba3133ec9aab 100644
--- a/modules/nf-core/mindagap/mindagap/tests/main.nf.test
+++ b/modules/nf-core/mindagap/mindagap/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['imaging']['tiff']['mouse_heart_wga'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'imaging/tiff/mindagap.mouse_heart.wga.tiff', checkIfExists: true)
                 ]
                 """
             }
@@ -33,4 +33,28 @@ nextflow_process {
 
     }
 
+    test("mindgap - tiff - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'imaging/tiff/mindagap.mouse_heart.wga.tiff', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-core/mindagap/mindagap/tests/main.nf.test.snap b/modules/nf-core/mindagap/mindagap/tests/main.nf.test.snap
index f799a144b53a..f75e48cf908b 100644
--- a/modules/nf-core/mindagap/mindagap/tests/main.nf.test.snap
+++ b/modules/nf-core/mindagap/mindagap/tests/main.nf.test.snap
@@ -1,4 +1,37 @@
 {
+    "mindgap - tiff - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "mindagap.mouse_heart.wga_gridfilled.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,937acaba2cb90efc2705b71839e6cefc"
+                ],
+                "tiff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "mindagap.mouse_heart.wga_gridfilled.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,937acaba2cb90efc2705b71839e6cefc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-02T19:54:00.036000058"
+    },
     "tiff": {
         "content": [
             [
@@ -10,6 +43,10 @@
                 ]
             ]
         ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
         "timestamp": "2023-12-15T11:01:20.825556802"
     },
     "versions": {
@@ -18,6 +55,10 @@
                 "versions.yml:md5,937acaba2cb90efc2705b71839e6cefc"
             ]
         ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
         "timestamp": "2023-12-15T11:01:20.840211732"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml
index 7a87bce9d706..1e4d674d6c7c 100644
--- a/modules/nf-core/modkit/pileup/environment.yml
+++ b/modules/nf-core/modkit/pileup/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - ont-modkit=0.3.0
+  - ont-modkit=0.4.3
diff --git a/modules/nf-core/modkit/pileup/main.nf b/modules/nf-core/modkit/pileup/main.nf
index f21a733f6677..7a3bb5e57799 100644
--- a/modules/nf-core/modkit/pileup/main.nf
+++ b/modules/nf-core/modkit/pileup/main.nf
@@ -4,12 +4,12 @@ process MODKIT_PILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ont-modkit:0.3.0--h5c23e0d_0':
-        'biocontainers/ont-modkit:0.3.0--h5c23e0d_0' }"
+        'https://depot.galaxyproject.org/singularity/ont-modkit:0.4.3--hcdda2d0_0':
+        'biocontainers/ont-modkit:0.4.3--hcdda2d0_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
-    tuple val(meta2), path(fasta)
+    tuple val(meta2), path(fasta), path(fai)
     tuple val(meta3), path(bed)
 
     output:
diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml
index 2f274d0c8cdd..ad259e816389 100644
--- a/modules/nf-core/modkit/pileup/meta.yml
+++ b/modules/nf-core/modkit/pileup/meta.yml
@@ -37,6 +37,10 @@ input:
         description: Reference sequence in FASTA format. Required for motif (e.g. CpG)
           filtering
         pattern: "*.fasta"
+    - fai:
+        type: file
+        description: Associated index file for FASTA
+        pattern: "*.fai"
   - - meta3:
         type: map
         description: |
diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test b/modules/nf-core/modkit/pileup/tests/main.nf.test
index 371cc3b94d49..6ce8dfe285b1 100644
--- a/modules/nf-core/modkit/pileup/tests/main.nf.test
+++ b/modules/nf-core/modkit/pileup/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
                 ]
-                input[1] = [[],[]]
+                input[1] = [[],[],[]]
                 input[2] = [[],[]]
                 """
             }
@@ -33,7 +33,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, []") {
+    test("[bam, bai], [fasta, fai], []") {
 
         when {
             process {
@@ -45,7 +45,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = [[],[]]
                 """
@@ -61,7 +62,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed") {
+    test("[bam, bai], [fasta, fai], bed") {
 
         when {
             process {
@@ -73,7 +74,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
@@ -91,7 +93,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed - traditional") {
+    test("[bam, bai], [fasta, fai], bed - traditional") {
 
         config "./nextflow.traditional.config"
 
@@ -105,7 +107,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
@@ -123,7 +126,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed - traditional, HP") {
+    test("[bam, bai], [fasta, fai], bed - traditional, HP") {
 
         config "./nextflow.traditional_hp.config"
 
@@ -137,7 +140,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
@@ -155,7 +159,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed - traditional, HP, bedgraph") {
+    test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph") {
 
         config "./nextflow.traditional_hp_bedgraph.config"
 
@@ -169,7 +173,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
@@ -199,7 +204,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
                 ]
-                input[1] = [[],[]]
+                input[1] = [[],[],[]]
                 input[2] = [[],[]]
                 """
             }
@@ -214,7 +219,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, [] - stub") {
+    test("[bam, bai], [fasta, fai], [] - stub") {
 
         options "-stub"
 
@@ -228,7 +233,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = [[],[]]
                 """
@@ -244,7 +250,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed - stub") {
+    test("[bam, bai], [fasta, fai], bed - stub") {
 
         options "-stub"
 
@@ -258,7 +264,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
@@ -276,7 +283,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed - traditional - stub") {
+    test("[bam, bai], [fasta, fai], bed - traditional - stub") {
 
         config "./nextflow.traditional.config"
         options "-stub"
@@ -291,7 +298,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
@@ -309,7 +317,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed - traditional, HP - stub") {
+    test("[bam, bai], [fasta, fai], bed - traditional, HP - stub") {
 
         config "./nextflow.traditional_hp.config"
         options "-stub"
@@ -324,7 +332,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
@@ -342,7 +351,7 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], fasta, bed - traditional, HP, bedgraph - stub") {
+    test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub") {
 
         config "./nextflow.traditional_hp_bedgraph.config"
         options "-stub"
@@ -357,7 +366,8 @@ nextflow_process {
                 ]
                 input[1] = [
                     [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 input[2] = Channel.of('chr22\t0\t1000')
                     .collectFile(name: 'chr22.bed', newLine: true)
diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
index b960409d2577..eefa7e6d667a 100644
--- a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
+++ b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
@@ -1,56 +1,5 @@
 {
-    "[bam, bai], fasta, bed - traditional, HP": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test_1.bed:md5,464a9870774c340753e79639aeaf76c2",
-                            "test_2.bed:md5,118de4b653dd082d76faa8802df493eb"
-                        ]
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test_1.bed:md5,464a9870774c340753e79639aeaf76c2",
-                            "test_2.bed:md5,118de4b653dd082d76faa8802df493eb"
-                        ]
-                    ]
-                ],
-                "bedgraph": [
-                    
-                ],
-                "log": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-10T09:09:40.272533628"
-    },
-    "[bam, bai], fasta, bed - traditional, HP, bedgraph - stub": {
+    "[bam, bai], [fasta, fai], [] - stub": {
         "content": [
             {
                 "0": [
@@ -78,7 +27,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
@@ -105,17 +54,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:11:33.234594142"
+        "timestamp": "2025-04-04T17:33:00.452010671"
     },
-    "[bam, bai], fasta, []": {
+    "[bam, bai], [fasta, fai], bed - traditional, HP": {
         "content": [
             {
                 "0": [
@@ -123,7 +72,10 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
+                        [
+                            "test_1.bed:md5,464a9870774c340753e79639aeaf76c2",
+                            "test_2.bed:md5,118de4b653dd082d76faa8802df493eb"
+                        ]
                     ]
                 ],
                 "1": [
@@ -133,14 +85,17 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
+                        [
+                            "test_1.bed:md5,464a9870774c340753e79639aeaf76c2",
+                            "test_2.bed:md5,118de4b653dd082d76faa8802df493eb"
+                        ]
                     ]
                 ],
                 "bedgraph": [
@@ -150,17 +105,17 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:09:03.537667806"
+        "timestamp": "2025-04-04T17:32:39.967304077"
     },
-    "[bam, bai], fasta, bed - traditional - stub": {
+    "[bam, bai], [], []": {
         "content": [
             {
                 "0": [
@@ -168,64 +123,44 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
                     ]
                 ],
                 "bedgraph": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "log": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:10:45.47904997"
+        "timestamp": "2025-04-04T18:20:59.925917273"
     },
-    "[bam, bai], fasta, bed - traditional, HP - stub": {
+    "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub": {
         "content": [
             {
                 "0": [
@@ -253,7 +188,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
@@ -280,17 +215,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:11:06.023194848"
+        "timestamp": "2025-04-04T17:33:30.43271761"
     },
-    "[bam, bai], fasta, [] - stub": {
+    "[bam, bai], [fasta, fai], bed - stub": {
         "content": [
             {
                 "0": [
@@ -318,7 +253,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
@@ -345,17 +280,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:10:17.995261822"
+        "timestamp": "2025-04-04T17:33:07.843477848"
     },
-    "[bam, bai], fasta, bed - stub": {
+    "[bam, bai], [fasta, fai], bed - traditional": {
         "content": [
             {
                 "0": [
@@ -363,64 +298,140 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed:md5,db6333f714a8ea4aa33902404a8d4812"
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
+                ],
+                "bed": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed:md5,db6333f714a8ea4aa33902404a8d4812"
                     ]
                 ],
-                "2": [
+                "bedgraph": [
+                    
+                ],
+                "log": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-04T17:32:32.191090081"
+    },
+    "[bam, bai], [fasta, fai], bed": {
+        "content": [
+            {
+                "0": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170"
                     ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170"
                     ]
                 ],
                 "bedgraph": [
+                    
+                ],
+                "log": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-04T17:32:24.40436977"
+    },
+    "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0",
+                            "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9"
+                        ]
                     ]
                 ],
-                "log": [
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
+                ],
+                "bed": [
+                    
+                ],
+                "bedgraph": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0",
+                            "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9"
+                        ]
                     ]
+                ],
+                "log": [
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:10:30.574897879"
+        "timestamp": "2025-04-04T17:32:47.765198075"
     },
-    "[bam, bai], [], []": {
+    "[bam, bai], [fasta, fai], []": {
         "content": [
             {
                 "0": [
@@ -438,7 +449,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
@@ -455,17 +466,17 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:08:51.291346508"
+        "timestamp": "2025-04-04T17:51:55.548559619"
     },
-    "[bam, bai], [], [] - stub": {
+    "[bam, bai], [fasta, fai], bed - traditional, HP - stub": {
         "content": [
             {
                 "0": [
@@ -493,7 +504,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
@@ -520,17 +531,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:10:05.670301111"
+        "timestamp": "2025-04-04T17:33:22.629911029"
     },
-    "[bam, bai], fasta, bed": {
+    "[bam, bai], [], [] - stub": {
         "content": [
             {
                 "0": [
@@ -538,95 +549,64 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170"
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
-                ],
-                "bed": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170"
+                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "bedgraph": [
-                    
-                ],
-                "log": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-10T09:09:15.042805699"
-    },
-    "[bam, bai], fasta, bed - traditional, HP, bedgraph": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
+                "2": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0",
-                            "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9"
-                        ]
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "2": [
-                    
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "bedgraph": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0",
-                            "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9"
-                        ]
+                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "log": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:09:52.968133216"
+        "timestamp": "2025-04-04T17:35:16.289350959"
     },
-    "[bam, bai], fasta, bed - traditional": {
+    "[bam, bai], [fasta, fai], bed - traditional - stub": {
         "content": [
             {
                 "0": [
@@ -634,41 +614,61 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,db6333f714a8ea4aa33902404a8d4812"
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "3": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ],
                 "bed": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,db6333f714a8ea4aa33902404a8d4812"
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "bedgraph": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "log": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe"
+                    "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-06-10T09:09:27.735400826"
+        "timestamp": "2025-04-04T17:33:15.218082198"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
index 97740c08e5d4..273c09bdd9bb 100644
--- a/modules/nf-core/muse/call/main.nf
+++ b/modules/nf-core/muse/call/main.nf
@@ -1,6 +1,6 @@
 process MUSE_CALL {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -33,7 +33,7 @@ process MUSE_CALL {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE //g" )
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE v//g")
     END_VERSIONS
     """
 
@@ -44,7 +44,7 @@ process MUSE_CALL {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE //g" )
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE v//g")
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/muse/call/tests/main.nf.test.snap b/modules/nf-core/muse/call/tests/main.nf.test.snap
index e9a0c0d9a6c3..bc826adcc639 100644
--- a/modules/nf-core/muse/call/tests/main.nf.test.snap
+++ b/modules/nf-core/muse/call/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,67bc768725ca9e5b73241808eda48eff"
+                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
                 ],
                 "txt": [
                     [
@@ -22,12 +22,12 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,67bc768725ca9e5b73241808eda48eff"
+                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
                 ]
             },
             {
                 "MUSE_CALL": {
-                    "MuSE": "v2.1.2"
+                    "MuSE": "2.1.2"
                 }
             }
         ],
@@ -35,12 +35,12 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-18T10:38:10.225172"
+        "timestamp": "2025-04-04T11:48:22.223976"
     },
     "human - bam": {
         "content": [
             [
-                "versions.yml:md5,67bc768725ca9e5b73241808eda48eff"
+                "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
             ],
             [
                 "##MuSE_call=\"MuSE -f genome.fasta -O test -n 2 call test2.paired_end.recalibrated.sorted.bam test.paired_end.recalibrated.sorted.bam\"",
@@ -78,6 +78,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-18T11:35:05.915076"
+        "timestamp": "2025-04-04T11:48:09.865014"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/muse/sump/main.nf b/modules/nf-core/muse/sump/main.nf
index 70b3352847c6..ac173142a082 100644
--- a/modules/nf-core/muse/sump/main.nf
+++ b/modules/nf-core/muse/sump/main.nf
@@ -1,19 +1,20 @@
 process MUSE_SUMP {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/35/3567f6162ff718c648175c5e7b5f848eaa27811d0cb3ad53def8f0a1c8893efa/data':
-        'community.wave.seqera.io/library/muse_tabix:df58ca78bd9447b7' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f9/f951cafbcec988c70d08bec486d40d902db4114bb1aaee89fd68155fdc3273da/data':
+        'community.wave.seqera.io/library/muse_tabix:cf4c19969fa62f63' }"
 
     input:
-    tuple val(meta), path(muse_call_txt)
+    tuple val(meta) , path(muse_call_txt)
     tuple val(meta2), path(ref_vcf), path(ref_vcf_tbi)
 
     output:
-    tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "versions.yml"              , emit: versions
+    tuple val(meta), path("*.vcf.gz")    , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,10 +33,11 @@ process MUSE_SUMP {
         -O ${prefix}.vcf
 
     bgzip $args2 --threads $task.cpus ${prefix}.vcf
+    tabix -p vcf ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE //g" )
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE v//g")
         bgzip: \$( bgzip --version | sed -n 's/bgzip (htslib) \\([0-9.]*\\)/\\1/p' )
     END_VERSIONS
     """
@@ -44,10 +46,11 @@ process MUSE_SUMP {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE //g" )
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" | sed -e "s/MuSE v//g")
         bgzip: \$( bgzip --version | sed -n 's/bgzip (htslib) \\([0-9.]*\\)/\\1/p' )
     END_VERSIONS
     """
diff --git a/modules/nf-core/muse/sump/meta.yml b/modules/nf-core/muse/sump/meta.yml
index 9e938e111408..1f5f38842cfc 100644
--- a/modules/nf-core/muse/sump/meta.yml
+++ b/modules/nf-core/muse/sump/meta.yml
@@ -51,11 +51,20 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-          pattern: "*.vcf"
       - "*.vcf.gz":
           type: map
           description: bgzipped vcf file with called variants
-          pattern: "*.vcf"
+          pattern: "*.vcf.gz"
+  - tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.vcf.gz.tbi":
+          type: map
+          description: tabix index of bgzipped vcf file with called variants
+          pattern: "*.vcf.gz.tbi"
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/muse/sump/tests/main.nf.test b/modules/nf-core/muse/sump/tests/main.nf.test
index 113fe8dd17c1..1364090fc9a8 100644
--- a/modules/nf-core/muse/sump/tests/main.nf.test
+++ b/modules/nf-core/muse/sump/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
 
         when {
             params {
-                module_args = '-E'
+                module_args = '-E' // '-G' for WGS data
             }
             process {
                 """
@@ -72,7 +72,7 @@ nextflow_process {
                 { assert snapshot(
                     process.out,
                     path(process.out.versions[0]).yaml
-                    ).match() 
+                    ).match()
                 }
             )
         }
diff --git a/modules/nf-core/muse/sump/tests/main.nf.test.snap b/modules/nf-core/muse/sump/tests/main.nf.test.snap
index 796bd3dc850e..18cff68b5495 100644
--- a/modules/nf-core/muse/sump/tests/main.nf.test.snap
+++ b/modules/nf-core/muse/sump/tests/main.nf.test.snap
@@ -11,7 +11,23 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b464e1a4b351fa27cea9141b8ab79bb7"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,83d9458549879e13641c6861a802aa31"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "vcf": [
                     [
@@ -22,12 +38,12 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b464e1a4b351fa27cea9141b8ab79bb7"
+                    "versions.yml:md5,83d9458549879e13641c6861a802aa31"
                 ]
             },
             {
                 "MUSE_SUMP": {
-                    "MuSE": "v2.1.2",
+                    "MuSE": "2.1.2",
                     "bgzip": 1.21
                 }
             }
@@ -36,12 +52,12 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-18T10:48:48.403588"
+        "timestamp": "2025-04-04T11:43:36.736512"
     },
     "human - txt": {
         "content": [
             [
-                "versions.yml:md5,b464e1a4b351fa27cea9141b8ab79bb7"
+                "versions.yml:md5,83d9458549879e13641c6861a802aa31"
             ],
             11,
             "VcfFile [chromosomes=[], sampleCount=2, variantCount=0, phased=true, phasedAutodetect=true]"
@@ -50,6 +66,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-18T10:48:40.369312"
+        "timestamp": "2025-04-04T11:57:11.337109"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/muse/sump/tests/nextflow.config b/modules/nf-core/muse/sump/tests/nextflow.config
index 6d29ad9187b1..96c26d581da7 100644
--- a/modules/nf-core/muse/sump/tests/nextflow.config
+++ b/modules/nf-core/muse/sump/tests/nextflow.config
@@ -2,11 +2,7 @@ process {
 
     withName: 'MUSE_SUMP' {
         ext.args    = params.module_args
-        stageInMode = 'copy'
-    }
-
-    withName: 'MUSE_SUMP_WGS' {
-        ext.args    = '-G'
+        stageInMode = 'copy' // to avoid that the dbsnp index is older than the dbsnp file
     }
 
 }
diff --git a/modules/nf-core/plink/indeppairwise/main.nf b/modules/nf-core/plink/indeppairwise/main.nf
index be6506ecacb6..1faaac7a5699 100644
--- a/modules/nf-core/plink/indeppairwise/main.nf
+++ b/modules/nf-core/plink/indeppairwise/main.nf
@@ -1,4 +1,3 @@
-
 process PLINK_INDEPPAIRWISE {
     tag "$meta.id"
     label 'process_low'
@@ -31,10 +30,24 @@ process PLINK_INDEPPAIRWISE {
         --bed ${bed}  \\
         --bim ${bim}  \\
         --fam ${fam}  \\
-        --threads $task.cpus \\
+        --threads ${task.cpus} \\
         --indep-pairwise ${window_size} ${variant_count} ${r2_threshold} \\
-        $args \\
-        --out $prefix
+        ${args} \\
+        --out ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.prune.in
+    touch ${prefix}.prune.out
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
diff --git a/modules/nf-core/plink/indeppairwise/tests/main.nf.test b/modules/nf-core/plink/indeppairwise/tests/main.nf.test
new file mode 100644
index 000000000000..b5df73699727
--- /dev/null
+++ b/modules/nf-core/plink/indeppairwise/tests/main.nf.test
@@ -0,0 +1,76 @@
+nextflow_process {
+
+    name "Test Process PLINK_INDEPPAIRWISE"
+    script "../main.nf"
+    process "PLINK_INDEPPAIRWISE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "plink"
+    tag "plink/indeppairwise"
+    tag "plink/vcf"
+
+    setup {
+
+        config "./nextflow.config"
+
+        params {
+            module_args = '--make-bed --biallelic-only strict --vcf-half-call haploid --allow-extra-chr'
+        }
+
+        run("PLINK_VCF") {
+
+            script "../../vcf/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz", checkIfExists:true)
+                    ]
+                """
+            }
+        }
+    }
+
+    test("test_plink_indeppairwise") {
+        when {
+            process {
+                """
+                input[0] = PLINK_VCF.out.bed.join(PLINK_VCF.out.bim).join(PLINK_VCF.out.fam)
+                input[1] = Channel.value(50)
+                input[2] = Channel.value(5)
+                input[3] = Channel.value(0.2)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_plink_indeppairwise - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = PLINK_VCF.out.bed.join(PLINK_VCF.out.bim).join(PLINK_VCF.out.fam)
+                input[1] = Channel.value(50)
+                input[2] = Channel.value(5)
+                input[3] = Channel.value(0.2)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/plink/indeppairwise/tests/main.nf.test.snap b/modules/nf-core/plink/indeppairwise/tests/main.nf.test.snap
new file mode 100644
index 000000000000..9e7b9e198293
--- /dev/null
+++ b/modules/nf-core/plink/indeppairwise/tests/main.nf.test.snap
@@ -0,0 +1,108 @@
+{
+    "test_plink_indeppairwise": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ],
+                "prunein": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,dce7ba75405107468f2ce18fc95a9786"
+                    ]
+                ],
+                "pruneout": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.out:md5,1f65f71308f2c4a03b9a4a98bbfb11e9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T14:55:08.717872783"
+    },
+    "test_plink_indeppairwise - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ],
+                "prunein": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.in:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pruneout": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.prune.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dd52fb8375a5ba36e766f25e9028d128"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-28T17:45:50.995416015"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/plink/indeppairwise/tests/nextflow.config b/modules/nf-core/plink/indeppairwise/tests/nextflow.config
new file mode 100644
index 000000000000..ffe075a1f57f
--- /dev/null
+++ b/modules/nf-core/plink/indeppairwise/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "PLINK_VCF" {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/plink2/filter/environment.yml b/modules/nf-core/plink2/filter/environment.yml
new file mode 100644
index 000000000000..e3c50dd73a9e
--- /dev/null
+++ b/modules/nf-core/plink2/filter/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::plink2=2.00a5.10
diff --git a/modules/nf-core/plink2/filter/main.nf b/modules/nf-core/plink2/filter/main.nf
new file mode 100644
index 000000000000..1018ca17e9bf
--- /dev/null
+++ b/modules/nf-core/plink2/filter/main.nf
@@ -0,0 +1,62 @@
+process PLINK2_FILTER {
+    tag "$meta.id"
+    label 'process_medium'
+
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/plink2:2.00a5.10--h4ac6f70_0':
+        'biocontainers/plink2:2.00a5.10--h4ac6f70_0' }"
+
+    input:
+    tuple val(meta), path(plink_genotype_file), path(plink_variant_file), path(plink_sample_file)
+
+    output:
+    tuple val(meta), path("*.bim"), emit: bim, optional: true
+    tuple val(meta), path("*.bed"), emit: bed, optional: true
+    tuple val(meta), path("*.fam"), emit: fam, optional: true
+    tuple val(meta), path("*.pgen"),emit: pgen, optional: true
+    tuple val(meta), path("*.psam"),emit: psam, optional: true
+    tuple val(meta), path("*.pvar"),emit: pvar, optional: true
+    path "versions.yml",            emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def mode = plink_genotype_file.extension == 'pgen' ? '--pfile' : '--bfile'
+    def outtype = plink_genotype_file.extension == "pgen" ? '--make-pgen' : '--make-bed'
+    def input = "${plink_genotype_file.getBaseName()}"
+    if( "${input}" == "${prefix}" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+
+    """
+    plink2 \\
+        $mode $input \\
+        $args \\
+        --threads $task.cpus \\
+        $outtype \\
+        --out $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def trio = plink_genotype_file.extension == 'pgen' ? "${prefix}.pfam ${prefix}.psam ${prefix}.pvar" : "${prefix}.bed ${prefix}.bim ${prefix}.fam"
+    if( "${plink_genotype_file.getBaseName()}" == "${prefix}" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch ${trio}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/nf-core/plink2/filter/meta.yml b/modules/nf-core/plink2/filter/meta.yml
new file mode 100644
index 000000000000..0ebb30b227ed
--- /dev/null
+++ b/modules/nf-core/plink2/filter/meta.yml
@@ -0,0 +1,122 @@
+---
+name: "plink2_filter"
+description: Filters plink bfiles or pfiles with filters such as maf or var
+keywords:
+  - plink2
+  - filter
+  - samples
+  - variants
+  - missingness
+  - qualty
+tools:
+  - "plink2":
+      description: |
+        Whole genome association analysis toolset, designed to perform a range
+        of basic, large-scale analyses in a computationally efficient manner
+      homepage: http://www.cog-genomics.org/plink/2.0/
+      documentation: http://www.cog-genomics.org/plink/2.0/general_usage
+      doi: "10.1186/s13742-015-0047-8"
+      licence: ["GPL v3"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - plink_genotype_file:
+        type: file
+        description: PLINK binary genotype table file or PLINK 2 binary genotype table file
+        pattern: "*.{bed,pgen}"
+        ontologies:
+          - edam: http://edamontology.org/format_3003
+    - plink_variant_file:
+        type: file
+        description: PLINK extended MAP file or PLINK 2 variant information file
+        pattern: "*.{bim,pvar}"
+    - plink_sample_file:
+        type: file
+        description: PLINK sample information file or PLINK 2 sample information file
+        pattern: "*.{fam,psam}"
+
+output:
+  - bed:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bed":
+          type: file
+          description: PLINK binary allelic genotype table
+          pattern: "*.bed"
+          ontologies:
+            - edam: http://edamontology.org/format_3003
+  - bim:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bim":
+          type: file
+          description: PLINK extended map file
+          pattern: "*.bim"
+          ontologies: []
+  - fam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fam":
+          type: file
+          description: PLINK sample information file
+          pattern: "*.fam"
+          ontologies: []
+  - pgen:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.pgen":
+          type: file
+          description: PLINK 2 binary genotype table
+          pattern: "*.pgen"
+          ontologies:
+            - edam: http://edamontology.org/format_3003
+  - pvar:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.pvar":
+          type: file
+          description: PLINK 2 variant information file
+          pattern: "*.pvar"
+          ontologies: []
+  - psam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.psam":
+          type: file
+          description: PLINK 2 sample information file
+          pattern: "*.psam"
+          ontologies: []
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+          ontologies: []
+
+authors:
+  - "@jodennehy"
+maintainers:
+  - "@jodennehy"
diff --git a/modules/nf-core/plink2/filter/tests/main.nf.test b/modules/nf-core/plink2/filter/tests/main.nf.test
new file mode 100644
index 000000000000..da99f8c8ba43
--- /dev/null
+++ b/modules/nf-core/plink2/filter/tests/main.nf.test
@@ -0,0 +1,191 @@
+nextflow_process {
+
+    name "Test Process PLINK2_FILTER"
+    script "../main.nf"
+    process "PLINK2_FILTER"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "plink2"
+    tag "plink2/filter"
+
+    test("plink1_input - var_filter") {
+
+        when {
+            params {
+                module_args = '--geno 0.05 --double-id'
+            }
+            process {
+
+                """
+
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("plink2_input - var_filter") {
+
+
+        when {
+            params {
+                module_args = '--geno 0.05 --double-id'
+            }
+            process {
+
+                """
+
+                input[0] = [
+                        [id:"test"],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pgen', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pvar', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.psam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("plink1_input - maf_filter") {
+
+        when {
+            params {
+                module_args = '--max-alleles 2 --double-id --maf 0.01'
+            }
+            process {
+
+                """
+
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("plink2_input - maf_filter") {
+
+
+        when {
+            params {
+                module_args = '--max-alleles 2 --double-id --maf 0.01'
+            }
+            process {
+
+                """
+
+                input[0] = [
+                        [id:"test"],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pgen', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pvar', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.psam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("plink1_input - var_filter - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = '--geno 0.05 --double-id'
+            }
+            process {
+                """
+
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("plink2_input - var_filter - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = '--geno 0.05 --double-id'
+            }
+            process {
+                """
+                input[0] = [
+                        [id:"test"],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pgen', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pvar', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.psam', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/plink2/filter/tests/main.nf.test.snap b/modules/nf-core/plink2/filter/tests/main.nf.test.snap
new file mode 100644
index 000000000000..99a686a48453
--- /dev/null
+++ b/modules/nf-core/plink2/filter/tests/main.nf.test.snap
@@ -0,0 +1,490 @@
+{
+    "plink2_input - var_filter": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pgen:md5,d37c6d0aa92f788705e98813907d197a"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psam:md5,dcecc49a20b9e2b26fe9883789908203"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pvar:md5,723cab01a7556da85d3594c1637ee5d4"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ],
+                "bed": [
+                    
+                ],
+                "bim": [
+                    
+                ],
+                "fam": [
+                    
+                ],
+                "pgen": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pgen:md5,d37c6d0aa92f788705e98813907d197a"
+                    ]
+                ],
+                "psam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psam:md5,dcecc49a20b9e2b26fe9883789908203"
+                    ]
+                ],
+                "pvar": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pvar:md5,723cab01a7556da85d3594c1637ee5d4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-09T13:37:14.224771"
+    },
+    "plink2_input - maf_filter": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pgen:md5,d37c6d0aa92f788705e98813907d197a"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psam:md5,dcecc49a20b9e2b26fe9883789908203"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pvar:md5,723cab01a7556da85d3594c1637ee5d4"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ],
+                "bed": [
+                    
+                ],
+                "bim": [
+                    
+                ],
+                "fam": [
+                    
+                ],
+                "pgen": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pgen:md5,d37c6d0aa92f788705e98813907d197a"
+                    ]
+                ],
+                "psam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psam:md5,dcecc49a20b9e2b26fe9883789908203"
+                    ]
+                ],
+                "pvar": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pvar:md5,723cab01a7556da85d3594c1637ee5d4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-09T13:37:32.740659"
+    },
+    "plink1_input - maf_filter": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bim:md5,41351028a80a8cf5bec0ab2db04af6c9"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,e1f17b70b8f213aa6d48dbde955451b4"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fam:md5,56314a08dc651daea82dd5b04da02d31"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,e1f17b70b8f213aa6d48dbde955451b4"
+                    ]
+                ],
+                "bim": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bim:md5,41351028a80a8cf5bec0ab2db04af6c9"
+                    ]
+                ],
+                "fam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fam:md5,56314a08dc651daea82dd5b04da02d31"
+                    ]
+                ],
+                "pgen": [
+                    
+                ],
+                "psam": [
+                    
+                ],
+                "pvar": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-09T13:37:23.654158"
+    },
+    "plink1_input - var_filter - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bim:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bim": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bim:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pgen": [
+                    
+                ],
+                "psam": [
+                    
+                ],
+                "pvar": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-09T13:37:46.079556"
+    },
+    "plink1_input - var_filter": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bim:md5,41351028a80a8cf5bec0ab2db04af6c9"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,e1f17b70b8f213aa6d48dbde955451b4"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fam:md5,56314a08dc651daea82dd5b04da02d31"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,e1f17b70b8f213aa6d48dbde955451b4"
+                    ]
+                ],
+                "bim": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bim:md5,41351028a80a8cf5bec0ab2db04af6c9"
+                    ]
+                ],
+                "fam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fam:md5,56314a08dc651daea82dd5b04da02d31"
+                    ]
+                ],
+                "pgen": [
+                    
+                ],
+                "psam": [
+                    
+                ],
+                "pvar": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-09T13:37:05.076078"
+    },
+    "plink2_input - var_filter - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pvar:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ],
+                "bed": [
+                    
+                ],
+                "bim": [
+                    
+                ],
+                "fam": [
+                    
+                ],
+                "pgen": [
+                    
+                ],
+                "psam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pvar": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pvar:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bfda17cbe28d98c1e1079188bde5e840"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-09T13:37:57.053175"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/plink2/filter/tests/nextflow.config b/modules/nf-core/plink2/filter/tests/nextflow.config
new file mode 100644
index 000000000000..e63b1f87ac9f
--- /dev/null
+++ b/modules/nf-core/plink2/filter/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: PLINK2_FILTER {
+        ext.args = params.module_args
+    }
+
+}
diff --git a/modules/nf-core/poolsnp/main.nf b/modules/nf-core/poolsnp/main.nf
index c292f395627e..fd05f85c2a40 100644
--- a/modules/nf-core/poolsnp/main.nf
+++ b/modules/nf-core/poolsnp/main.nf
@@ -10,7 +10,7 @@ process POOLSNP {
     input:
     tuple val(meta) , path(mpileup)
     tuple val(meta2), path(reference)
-    tuple val(meta) , val(max_cov), path(max_cov_file)
+    tuple val(meta3), val(max_cov), path(max_cov_file)
 
     output:
     tuple val(meta), path("*.vcf.gz")  , emit: vcf
@@ -44,7 +44,6 @@ process POOLSNP {
     """
 
     stub:
-    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
diff --git a/modules/nf-core/poolsnp/meta.yml b/modules/nf-core/poolsnp/meta.yml
index 36054b58aca6..9d58fc2e34d8 100644
--- a/modules/nf-core/poolsnp/meta.yml
+++ b/modules/nf-core/poolsnp/meta.yml
@@ -40,7 +40,7 @@ input:
           Reference genome in FASTA format.
           May NOT contain any special characters such as "/|,:"
         pattern: "*.{fasta,fa}"
-  - - meta:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing sample information.
diff --git a/modules/nf-core/poolsnp/tests/main.nf.test.snap b/modules/nf-core/poolsnp/tests/main.nf.test.snap
index f908d02916c5..8ac27c890a2a 100644
--- a/modules/nf-core/poolsnp/tests/main.nf.test.snap
+++ b/modules/nf-core/poolsnp/tests/main.nf.test.snap
@@ -8,17 +8,18 @@
             [
                 [
                     {
-                        "id": "test"
+                        "id": "test",
+                        "single_end": false
                     },
                     "test_cov-0.7.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-16T15:51:10.298893"
+        "timestamp": "2025-04-05T11:57:13.661565"
     },
     "sarscov2 - mpileup - max_cov_file - stub": {
         "content": [
@@ -42,17 +43,18 @@
             [
                 [
                     {
-                        "id": "test"
+                        "id": "test",
+                        "single_end": false
                     },
                     "test-cov-0.7.txt:md5,ccbb119522c09daa976a9015ba999329"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-16T15:30:50.011"
+        "timestamp": "2025-04-05T11:56:50.034677"
     },
     "sarscov2 - mpileup - max_cov_file": {
         "content": [
diff --git a/modules/nf-core/porechop/abi/main.nf b/modules/nf-core/porechop/abi/main.nf
index 88ec5bd0ea95..e9205e0c70fc 100644
--- a/modules/nf-core/porechop/abi/main.nf
+++ b/modules/nf-core/porechop/abi/main.nf
@@ -9,6 +9,7 @@ process PORECHOP_ABI {
 
     input:
     tuple val(meta), path(reads)
+    path custom_adapters
 
     output:
     tuple val(meta), path("*.fastq.gz") , emit: reads
@@ -21,10 +22,12 @@ process PORECHOP_ABI {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi"
+    def adapters_list = custom_adapters ? "--custom_adapters ${custom_adapters}" : ""
     if ("$reads" == "${prefix}.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     porechop_abi \\
         --input $reads \\
+        $adapters_list \\
         --threads $task.cpus \\
         $args \\
         --output ${prefix}.fastq.gz \\
@@ -38,6 +41,7 @@ process PORECHOP_ABI {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi"
+    def adapters_list = custom_adapters ? "--custom_adapters ${custom_adapters}" : ""
     """
     echo "" | gzip > ${prefix}.fastq.gz
     touch ${prefix}.log
diff --git a/modules/nf-core/porechop/abi/meta.yml b/modules/nf-core/porechop/abi/meta.yml
index 6016da7560f5..bff17e64f8e9 100644
--- a/modules/nf-core/porechop/abi/meta.yml
+++ b/modules/nf-core/porechop/abi/meta.yml
@@ -25,6 +25,10 @@ input:
         type: file
         description: fastq/fastq.gz file
         pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
+  - - custom_adapters:
+        type: file
+        description: Text file containing custom adapters
+
 output:
   - reads:
       - meta:
diff --git a/modules/nf-core/porechop/abi/tests/main.nf.test b/modules/nf-core/porechop/abi/tests/main.nf.test
index b5a29f908461..23e34d7de4a0 100644
--- a/modules/nf-core/porechop/abi/tests/main.nf.test
+++ b/modules/nf-core/porechop/abi/tests/main.nf.test
@@ -17,6 +17,7 @@ nextflow_process {
                     [ id:'test'], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
                 ]
+		input[1] = []
                 """
             }
         }
@@ -45,6 +46,7 @@ nextflow_process {
                     [ id:'test'], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
                 ]
+		input[1] = []
                 """
             }
         }
diff --git a/modules/nf-core/porechop/abi/tests/main.nf.test.snap b/modules/nf-core/porechop/abi/tests/main.nf.test.snap
index ad63f4edb9b8..5fc4d0603df3 100644
--- a/modules/nf-core/porechop/abi/tests/main.nf.test.snap
+++ b/modules/nf-core/porechop/abi/tests/main.nf.test.snap
@@ -37,10 +37,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-07-29T13:50:49.318599"
+        "timestamp": "2025-04-10T10:27:24.536642628"
     },
     "sarscov2-nanopore - stub": {
         "content": [
@@ -86,9 +86,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-07-29T13:50:54.425389"
+        "timestamp": "2025-04-10T10:27:30.502715737"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/porechop/porechop/environment.yml b/modules/nf-core/porechop/porechop/environment.yml
index b2696aeddff2..109cf8bd68fa 100644
--- a/modules/nf-core/porechop/porechop/environment.yml
+++ b/modules/nf-core/porechop/porechop/environment.yml
@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::porechop=0.2.4
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/porechop/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf
index 1ff02a12a520..34daf3e8951f 100644
--- a/modules/nf-core/porechop/porechop/main.nf
+++ b/modules/nf-core/porechop/porechop/main.nf
@@ -3,9 +3,10 @@ process PORECHOP_PORECHOP {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
-        'biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?        
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2bce1f10c51906a66c4c4d3a7485394f67e304177192ad1cce6cf586a3a18bae/data' :
+        'community.wave.seqera.io/library/porechop_pigz:d1655e5b5bad786c' }"
+
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/portcullis/full/main.nf b/modules/nf-core/portcullis/full/main.nf
index 22628713920b..96a05b306c47 100644
--- a/modules/nf-core/portcullis/full/main.nf
+++ b/modules/nf-core/portcullis/full/main.nf
@@ -13,10 +13,14 @@ process PORTCULLIS_FULL {
     tuple val(meta3), path(fasta)
 
     output:
-    tuple val(meta), path("*.log"), emit: log
-    tuple val(meta), path("*.bed"), emit: bed
-    tuple val(meta), path("*.tab"), emit: tab
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.pass.junctions.bed"), emit: pass_junctions_bed
+    tuple val(meta), path("*.pass.junctions.tab"), emit: pass_junctions_tab
+    tuple val(meta), path("*.portcullis.log")    , emit: log
+    tuple val(meta), path("*.intron.gff3")       , emit: intron_gff , optional: true
+    tuple val(meta), path("*.exon.gff3")         , emit: exon_gff   , optional: true
+    tuple val(meta), path("*.bam")               , emit: spliced_bam, optional: true
+    tuple val(meta), path("*.bai")               , emit: spliced_bai, optional: true
+    path "versions.yml"                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,8 +38,18 @@ process PORTCULLIS_FULL {
         $fasta \\
         $bam > ${prefix}.portcullis.log
 
-    cp ${prefix}/3-filt/*.bed .
-    cp ${prefix}/3-filt/*.tab .
+    cp ${prefix}/3-filt/*.pass.junctions.bed .
+    cp ${prefix}/3-filt/*.pass.junctions.tab .
+    if [ -f ${prefix}/3-filt/*.pass.junctions.intron.gff3 ] ; then
+        cp ${prefix}/3-filt/*.pass.junctions.intron.gff3 .
+    fi
+    if [ -f ${prefix}/3-filt/*.pass.junctions.exon.gff3 ] ; then
+        cp ${prefix}/3-filt/*.pass.junctions.exon.gff3 .
+    fi
+    if [ -f ${prefix}/2-junc/*.spliced.bam ] ; then
+        cp ${prefix}/2-junc/*.spliced.bam.bai .
+        cp ${prefix}/2-junc/*.spliced.bam .
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -48,8 +62,8 @@ process PORTCULLIS_FULL {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.portcullis.log
-    touch ${prefix}.portcullis.bed
-    touch ${prefix}.portcullis.tab
+    touch ${prefix}.pass.junctions.bed
+    touch ${prefix}.pass.junctions.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/portcullis/full/meta.yml b/modules/nf-core/portcullis/full/meta.yml
index d67743c81744..c6a5f87cb958 100644
--- a/modules/nf-core/portcullis/full/meta.yml
+++ b/modules/nf-core/portcullis/full/meta.yml
@@ -9,8 +9,8 @@ tools:
   - "portcullis":
       description: "Portcullis is a tool that filters out invalid splice junctions from
         RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes
-        splice junctions and removes likely false positives, outputting filtered
-        results in multiple formats for downstream analysis."
+        splice junctions and removes likely false positives, outputting filtered results
+        in multiple formats for downstream analysis."
       homepage: "https://portcullis.readthedocs.io/en/latest/index.html"
       documentation: "https://portcullis.readthedocs.io/en/latest/using.html"
       doi: "10.1101/217620"
@@ -58,43 +58,92 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*.log"
-      - "*.log":
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.portcullis.log":
           type: file
           description: Log file containing Portcullis execution details, processing steps,
             and filtering statistics
           pattern: "*.log"
           ontologies:
             - edam: "http://edamontology.org/format_2330"
-  - bed:
+  - pass_junctions_bed:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*.bed"
-      - "*.bed":
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.pass.junctions.bed":
           type: file
           description: |
             Filtered splice junction coordinates in BED format, containing genomic coordinates of valid splice junctions after filtering out false positives
-          pattern: "*.bed"
+          pattern: "*.pass.junctions.bed"
           ontologies:
             - edam: "http://edamontology.org/format_3003"
-  - tab:
+  - pass_junctions_tab:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-          pattern: "*.tab"
-      - "*.tab":
-          type: map
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.pass.junctions.tab":
+          type: file
           description: |
             Tabular representation of filtered splice junctions with additional metrics including junction scores, read support, and filtering decision data
-          pattern: "*.tab"
+          pattern: "*.pass.junctions.tab"
           ontologies:
             - eadam: "http://edamontology.org/format_3475"
+  - intron_gff:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.intron.gff3":
+          type: file
+          description: |
+            Output intron-based junctions in GFF format.
+          pattern: "*.intron.gff3"
+          ontologies:
+            - edam: "http://edamontology.org/format_1975"
+  - exon_gff:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.exon.gff3":
+          type: file
+          description: |
+            Output exon-based junctions in GFF format.
+          pattern: "*.exon.gff3"
+          ontologies:
+            - edam: "http://edamontology.org/format_1975"
+  - spliced_bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.bam":
+          type: file
+          description: |
+            BAM file after filtering original BAM file by removing alignments associated with bad junctions
+          pattern: "*.bam"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572"
+  - spliced_bai:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.bai":
+          type: file
+          description: |
+            Index of the output BAM file
+          pattern: "*.bai"
+          ontologies:
+            - edam: "http://edamontology.org/format_3327"
   - versions:
       - versions.yml:
           type: file
@@ -106,3 +155,4 @@ authors:
   - "@jblancoheredia"
 maintainer:
   - "@jblancoheredia"
+  - "@anoronh4"
diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test b/modules/nf-core/portcullis/full/tests/main.nf.test
index fe7e9ff06dc1..e98d3dc99cb5 100644
--- a/modules/nf-core/portcullis/full/tests/main.nf.test
+++ b/modules/nf-core/portcullis/full/tests/main.nf.test
@@ -10,6 +10,7 @@ nextflow_process {
     tag "portcullis/full"
 
     test("portcullis_full_paired_end") {
+        config "./nextflow.config"
 
         when {
             process {
@@ -33,9 +34,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert file(process.out.spliced_bam.get(0).get(1)).name == "portcullis_all.spliced.bam" },
+                { assert file(process.out.spliced_bai.get(0).get(1)).name == "portcullis_all.spliced.bam.bai" },
                 { assert snapshot(
-                    process.out.bed,
-                    process.out.tab,
+                    process.out.pass_junctions_bed,
+                    process.out.pass_junctions_tab,
+                    process.out.intron_gff,
+                    process.out.exon_gff,
                     process.out.versions
                     ).match()
                 }
@@ -70,8 +75,10 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bed,
-                    process.out.tab,
+                    process.out.pass_junctions_bed,
+                    process.out.pass_junctions_tab,
+                    process.out.intron_gff,
+                    process.out.exon_gff,
                     process.out.versions
                     ).match()
                 }
diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test.snap b/modules/nf-core/portcullis/full/tests/main.nf.test.snap
index 995bed3e85f8..8ee19487bf26 100644
--- a/modules/nf-core/portcullis/full/tests/main.nf.test.snap
+++ b/modules/nf-core/portcullis/full/tests/main.nf.test.snap
@@ -7,10 +7,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    [
-                        "portcullis_filtered.pass.junctions.bed:md5,613288f6b446359fd0153a7e628e1489",
-                        "portcullis_filtered.rules_in.junctions.bed:md5,572427ab6ea0832a1810ed1e706d3920"
-                    ]
+                    "portcullis_filtered.pass.junctions.bed:md5,613288f6b446359fd0153a7e628e1489"
                 ]
             ],
             [
@@ -19,12 +16,25 @@
                         "id": "test",
                         "single_end": false
                     },
-                    [
-                        "portcullis_filtered.pass.junctions.tab:md5,6e2dd7e93f6b7a23d90d3c3c11e99085",
-                        "portcullis_filtered.rules_in.junctions.tab:md5,6e1aaeb5f73b94142cfa9794d7470a6c",
-                        "portcullis_filtered.rules_out.failed.junctions.tab:md5,be919d60ca646342f6edc2f530174353",
-                        "portcullis_filtered.rules_out.passed.junctions.tab:md5,725bc8ad2a2e8e8456123e25cbb5541b"
-                    ]
+                    "portcullis_filtered.pass.junctions.tab:md5,6e2dd7e93f6b7a23d90d3c3c11e99085"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "portcullis_filtered.pass.junctions.intron.gff3:md5,3ee2c3526bfb54f81bfd55a3ab679570"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "portcullis_filtered.pass.junctions.exon.gff3:md5,7a3c56aca8dcd39ee2dec40589511a81"
                 ]
             ],
             [
@@ -33,9 +43,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2025-03-07T08:45:09.959686"
+        "timestamp": "2025-04-01T11:06:43.691683"
     },
     "portcullis_full_paired_end_stub": {
         "content": [
@@ -45,7 +55,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.portcullis.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.pass.junctions.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
             [
@@ -54,8 +64,14 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.portcullis.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.pass.junctions.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
+            ],
+            [
+                
+            ],
+            [
+                
             ],
             [
                 "versions.yml:md5,b297b098450e5baaea436e822fe25b0e"
@@ -63,8 +79,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2025-03-07T08:45:14.189846"
+        "timestamp": "2025-04-01T11:06:52.265624"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/portcullis/full/tests/nextflow.config b/modules/nf-core/portcullis/full/tests/nextflow.config
new file mode 100644
index 000000000000..671cdd5bcd4b
--- /dev/null
+++ b/modules/nf-core/portcullis/full/tests/nextflow.config
@@ -0,0 +1,11 @@
+process {
+    withName: PORTCULLIS_FULL {
+        ext.args = {
+            [
+                "--intron_gff",
+                "--exon_gff",
+                "--separate"
+            ].join(" ").trim()
+        }
+    }
+}
diff --git a/modules/nf-core/propr/propd/meta.yml b/modules/nf-core/propr/propd/meta.yml
index 57f1521f15f9..ba7a7a2fefa9 100644
--- a/modules/nf-core/propr/propd/meta.yml
+++ b/modules/nf-core/propr/propd/meta.yml
@@ -58,13 +58,13 @@ output:
       - meta:
           type: file
           description: |
-            TSV-format table of genes associated with differential expression 
+            TSV-format table of genes associated with differential expression
             information as compiled from the propd results
           pattern: "*.propd.genewise.tsv"
       - "*.propd.genewise.tsv":
           type: file
           description: |
-            TSV-format table of genes associated with differential expression 
+            TSV-format table of genes associated with differential expression
             information as compiled from the propd results
           pattern: "*.propd.genewise.tsv"
   - genewise_plot:
@@ -97,15 +97,15 @@ output:
       - meta:
           type: file
           description: |
-            (Optional) TSV-format table of the native propd pairwise results. This 
-            table contains the differential proportionality values associated to 
+            (Optional) TSV-format table of the native propd pairwise results. This
+            table contains the differential proportionality values associated to
             each pair of genes.
           pattern: "*.propd.pairwise.tsv"
       - "*.propd.pairwise.tsv":
           type: file
           description: |
-            (Optional) TSV-format table of the native propd pairwise results. This 
-            table contains the differential proportionality values associated to 
+            (Optional) TSV-format table of the native propd pairwise results. This
+            table contains the differential proportionality values associated to
             each pair of genes.
           pattern: "*.propd.pairwise.tsv"
   - results_pairwise_filtered:
@@ -113,28 +113,28 @@ output:
           type: file
           description: |
             (Optional) TSV-format table of the filtered propd pairwise results. This
-            table contains the pairs of genes with significant differential 
+            table contains the pairs of genes with significant differential
             proportionality values.
           pattern: "*.propd.pairwise_filtered.tsv"
       - "*.propd.pairwise_filtered.tsv":
           type: file
           description: |
             (Optional) TSV-format table of the filtered propd pairwise results. This
-            table contains the pairs of genes with significant differential 
+            table contains the pairs of genes with significant differential
             proportionality values.
           pattern: "*.propd.pairwise_filtered.tsv"
   - adjacency:
       - meta:
           type: file
           description: |
-            (Optional) CSV-format table of the adjacency matrix defining a graph, with 
+            (Optional) CSV-format table of the adjacency matrix defining a graph, with
             edges (1) associated to pairs of genes that are significantly differentially
             proportional.
           pattern: "*.propd.adjacency.csv"
       - "*.propd.adjacency.csv":
           type: file
           description: |
-            (Optional) CSV-format table of the adjacency matrix defining a graph, with 
+            (Optional) CSV-format table of the adjacency matrix defining a graph, with
             edges (1) associated to pairs of genes that are significantly differentially
             proportional.
           pattern: "*.propd.adjacency.csv"
diff --git a/modules/nf-core/ragtag/patch/environment.yml b/modules/nf-core/ragtag/patch/environment.yml
new file mode 100644
index 000000000000..83cefc79e8da
--- /dev/null
+++ b/modules/nf-core/ragtag/patch/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::ragtag=2.1.0"
diff --git a/modules/nf-core/ragtag/patch/main.nf b/modules/nf-core/ragtag/patch/main.nf
new file mode 100644
index 000000000000..4e8cf4558179
--- /dev/null
+++ b/modules/nf-core/ragtag/patch/main.nf
@@ -0,0 +1,109 @@
+process RAGTAG_PATCH {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/ragtag:2.1.0--pyhb7b1952_0'
+        : 'biocontainers/ragtag:2.1.0--pyhb7b1952_0'}"
+
+    input:
+    tuple val(meta), path(target, name: 'target/*') 
+    tuple val(meta2), path(query, name: 'query/*')
+    tuple val(meta3), path(exclude)
+    tuple val(meta4), path(skip)
+    
+    output:
+    tuple val(meta), path("*.patch.fasta"),         emit: patch_fasta
+    tuple val(meta), path("*.patch.agp"),           emit: patch_agp
+    tuple val(meta), path("*.comps.fasta"),         emit: patch_components_fasta
+    tuple val(meta), path("*.ragtag.patch.asm.*"),  emit: assembly_alignments,      optional: true
+    tuple val(meta), path("*.ctg.agp"),             emit: target_splits_agp
+    tuple val(meta), path("*.ctg.fasta"),           emit: target_splits_fasta
+    tuple val(meta), path("*.rename.agp"),          emit: qry_rename_agp,           optional: true
+    tuple val(meta), path("*.rename.fasta"),        emit: qry_rename_fasta,         optional: true
+    tuple val(meta), path("*.patch.err"),           emit: stderr
+    path "versions.yml",                            emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ""
+    def arg_exclude = exclude ? "-e ${exclude}" : ""
+    def arg_skip = skip ? "-j ${skip}" : ""
+    """
+    if [[ ${target} == *.gz ]]
+    then
+        zcat ${target} > target.fa
+    else
+        ln -s ${target} target.fa
+    fi
+
+    if [[ ${query} == *.gz ]]
+    then
+        zcat ${query} > query.fa
+    else
+        ln -s ${query} query.fa
+    fi
+
+    tail -F ${prefix}/ragtag.patch.err >&2 &
+    tailpid=\$!
+    ragtag.py patch target.fa query.fa \\
+        -o "${prefix}" \\
+        -t ${task.cpus} \\
+        ${arg_exclude} \\
+        ${arg_skip} \\
+        ${args} \\
+        2> >( tee ${prefix}.stderr.log >&2 ) \\
+         | tee ${prefix}.stdout.log
+
+    kill -TERM "\$tailpid"
+
+    mv ${prefix}/ragtag.patch.agp ${prefix}.patch.agp
+    mv ${prefix}/ragtag.patch.fasta ${prefix}.patch.fasta
+    mv ${prefix}/ragtag.patch.comps.fasta ${prefix}.comps.fasta
+    mv ${prefix}/ragtag.patch.ctg.agp ${prefix}.ctg.agp
+    mv ${prefix}/ragtag.patch.ctg.fasta ${prefix}.ctg.fasta
+    if [ -f ${prefix}/ragtag.patch.rename.agp ]; then
+        mv ${prefix}/ragtag.patch.rename.agp ${prefix}.rename.agp
+    fi
+
+    if [ -f ${prefix}/ragtag.patch.rename.fasta ]; then
+        mv ${prefix}/ragtag.patch.rename.fasta ${prefix}.rename.fasta
+    fi
+    mv ${prefix}/ragtag.patch.err ${prefix}.patch.err
+    # Move the assembly files from prefix folder, and add prefix
+    for alignment_file in \$(ls ${prefix}/ragtag.patch.asm.*);
+        do 
+            mv "\$alignment_file" "\${alignment_file/${prefix}\\//${prefix}_}"
+        done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ragtag: \$(echo \$(ragtag.py -v | sed 's/v//'))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def _args = task.ext.args ?: ""
+    def _arg_exclude = exclude ? "-e ${exclude}" : ""
+    def _arg_skip = skip ? "-j ${skip}" : ""
+    """
+    touch ${prefix}.patch.agp
+    touch ${prefix}.patch.fasta
+    touch ${prefix}.comps.fasta
+    touch ${prefix}.ctg.agp
+    touch ${prefix}.ctg.fasta
+    touch ${prefix}.rename.agp
+    touch ${prefix}.rename.fasta
+    touch ${prefix}.ragtag.patch.asm.1
+    touch ${prefix}.patch.err
+    
+    cat <<-END_VERSIONS > versions.yml
+        ragtag: \$(echo \$(ragtag.py -v | sed 's/v//'))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/ragtag/patch/meta.yml b/modules/nf-core/ragtag/patch/meta.yml
new file mode 100644
index 000000000000..d74ee3d20402
--- /dev/null
+++ b/modules/nf-core/ragtag/patch/meta.yml
@@ -0,0 +1,156 @@
+name: "ragtag_patch"
+description: "Homology-based assembly patching: Make continuous joins and fill gaps
+  in 'target.fa' using sequences from 'query.fa'"
+
+keywords:
+  - assembly
+  - consensus
+  - ragtag
+  - patch
+tools:
+  - "ragtag":
+      description: "Fast reference-guided genome assembly scaffolding"
+      homepage: "https://github.com/malonge/RagTag/wiki"
+      documentation: "https://github.com/malonge/RagTag/wiki"
+      tool_dev_url: "https://github.com/malonge/RagTag"
+      doi: "10.1186/s13059-022-02823-7"
+      licence: ["MIT"]
+      identifier: biotools:ragtag
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - target:
+        type: file
+        description: Target assembly
+        pattern: "*.{fasta,fasta.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - query:
+        type: file
+        description: Query assembly
+        pattern: "*.{fasta,fasta.gz}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - exclude:
+        type: file
+        description: list of target sequences to ignore
+        pattern: "*.txt"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - skip:
+        type: file
+        description: list of query sequences to ignore
+        pattern: "*.txt"
+output:
+  - patch_fasta:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.patch.fasta":
+          type: file
+          description: FASTA file containing the patched assembly
+          pattern: "*.patch.fasta"
+  - patch_agp:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.patch.agp":
+          type: file
+          description: AGP file defining how ragtag.patch.fasta is built
+          pattern: "*.patch.agp"
+  - patch_components_fasta:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.comps.fasta":
+          type: file
+          description: The split target assembly and the renamed query assembly combined
+            into one FASTA file. This file contains all components in ragtag.patch.agp
+          pattern: "*.comps.fasta"
+  - assembly_alignments:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.ragtag.patch.asm.*":
+          type: file
+          description: Assembly alignment files
+          pattern: "*.ragtag.patch.asm.*"
+  - target_splits_agp:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.ctg.agp":
+          type: file
+          description: An AGP file defining how the target assembly was split at gaps
+          pattern: "*.ctg.agp"
+  - target_splits_fasta:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.ctg.fasta":
+          type: file
+          description: FASTA file containing the target assembly split at gaps
+          pattern: "*.ctg.fasta"
+  - qry_rename_agp:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.rename.agp":
+          type: file
+          description: An AGP file defining the new names for query sequences
+          pattern: "*.rename.agp"
+  - qry_rename_fasta:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.rename.fasta":
+          type: file
+          description: A FASTA file with the original query sequence, but with new names
+          pattern: "*.rename.fasta"
+  - stderr:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.patch.err":
+          type: file
+          description: Standard error logging for all external RagTag commands
+          pattern: "*.patch.err"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@nschan"
+maintainers:
+  - "@nschan"
diff --git a/modules/nf-core/ragtag/patch/tests/main.nf.test b/modules/nf-core/ragtag/patch/tests/main.nf.test
new file mode 100644
index 000000000000..a7c0fee80b66
--- /dev/null
+++ b/modules/nf-core/ragtag/patch/tests/main.nf.test
@@ -0,0 +1,89 @@
+nextflow_process {
+
+    name "Test Process RAGTAG_PATCH"
+    script "../main.nf"
+    process "RAGTAG_PATCH"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ragtag"
+    tag "ragtag/patch"
+
+
+test("A. thaliana Col-0 test data - ragtag - patch") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[2] = [
+                    [],
+                    []
+                ]
+                input[3] = [
+                    [],
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.patch_fasta,
+                    process.out.patch_agp,
+                    process.out.patch_components_fasta,
+                    process.out.target_splits_agp,
+                    process.out.target_splits_fasta,
+                    process.out.versions
+                    ).match()
+                },
+            )
+        }
+
+    }
+    test("A. thaliana Col-0 test data - ragtag - patch - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[2] = [
+                    [],
+                    []
+                ]
+                input[3] = [
+                    [],
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/ragtag/patch/tests/main.nf.test.snap b/modules/nf-core/ragtag/patch/tests/main.nf.test.snap
new file mode 100644
index 000000000000..b144469262da
--- /dev/null
+++ b/modules/nf-core/ragtag/patch/tests/main.nf.test.snap
@@ -0,0 +1,215 @@
+{
+    "A. thaliana Col-0 test data - ragtag - patch - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.patch.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.patch.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.comps.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ragtag.patch.asm.1:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ctg.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ctg.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.rename.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.rename.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,cecbb39907d607affa6522e395b78a1f"
+                ],
+                "assembly_alignments": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ragtag.patch.asm.1:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "patch_agp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.patch.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "patch_components_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.comps.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "patch_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.patch.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "qry_rename_agp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.rename.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "qry_rename_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.rename.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stderr": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "target_splits_agp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ctg.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "target_splits_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ctg.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cecbb39907d607affa6522e395b78a1f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-04T14:10:01.648597527"
+    },
+    "A. thaliana Col-0 test data - ragtag - patch": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.patch.fasta:md5,5cf615df690061ab15e4fee62abf3ebc"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.patch.agp:md5,7878fd4e42ecb2bfccd7565d5ed6b625"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.comps.fasta:md5,65bd2563dfc2564d5edf0e8d24257032"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.ctg.agp:md5,ac3460a377daaf3e3ce37f499e561968"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.ctg.fasta:md5,5cf615df690061ab15e4fee62abf3ebc"
+                ]
+            ],
+            [
+                "versions.yml:md5,4c0992a27edf294209711ce4f181eb5a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-04T14:25:42.121285998"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ragtag/scaffold/environment.yml b/modules/nf-core/ragtag/scaffold/environment.yml
new file mode 100644
index 000000000000..83cefc79e8da
--- /dev/null
+++ b/modules/nf-core/ragtag/scaffold/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::ragtag=2.1.0"
diff --git a/modules/nf-core/ragtag/scaffold/main.nf b/modules/nf-core/ragtag/scaffold/main.nf
new file mode 100644
index 000000000000..c3930c12e846
--- /dev/null
+++ b/modules/nf-core/ragtag/scaffold/main.nf
@@ -0,0 +1,82 @@
+process RAGTAG_SCAFFOLD {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/ragtag:2.1.0--pyhb7b1952_0'
+        : 'biocontainers/ragtag:2.1.0--pyhb7b1952_0'}"
+
+    input:
+    tuple val(meta), path(assembly, name: 'assembly/*')
+    tuple val(meta2), path(reference, name: 'reference/*')
+    tuple val(meta3), path(exclude)
+    tuple val(meta4), path(skip), path(hard_skip)
+
+    output:
+    tuple val(meta), path("*.fasta"),   emit: corrected_assembly
+    tuple val(meta), path("*.agp"),     emit: corrected_agp
+    tuple val(meta), path("*.stats"),   emit: corrected_stats
+    path "versions.yml",                emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def arg_exclude = exclude ? "-e ${exclude}" : ""
+    def arg_skip = skip ? "-j ${skip}" : ""
+    def arg_hard_skip = hard_skip ? "-J ${hard_skip}" : ""
+    """
+    if [[ ${assembly} == *.gz ]]
+    then
+        zcat ${assembly} > assembly.fa
+    else
+        ln -s ${assembly} assembly.fa
+    fi
+
+    if [[ ${reference} == *.gz ]]
+    then
+        zcat ${reference} > reference.fa
+    else
+        ln -s ${reference} reference.fa
+    fi
+
+    ragtag.py scaffold reference.fa assembly.fa \\
+        -o "${prefix}" \\
+        -t ${task.cpus} \\
+        -C \\
+        ${arg_exclude} \\
+        ${arg_skip} \\
+        ${arg_hard_skip} \\
+        ${args} \\
+        2> >( tee ${prefix}.stderr.log >&2 ) \\
+        | tee ${prefix}.stdout.log
+
+    mv ${prefix}/ragtag.scaffold.fasta ${prefix}.fasta
+    mv ${prefix}/ragtag.scaffold.agp ${prefix}.agp
+    mv ${prefix}/ragtag.scaffold.stats ${prefix}.stats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ragtag: \$(echo \$(ragtag.py -v | sed 's/v//'))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def _args = task.ext.args ?: ''
+    def _arg_exclude = exclude ? "-e ${exclude}" : ""
+    def _arg_skip = skip ? "-j ${skip}" : ""
+    def _arg_hard_skip = hard_skip ? "-J ${hard_skip}" : ""
+    """
+    touch ${prefix}.fasta
+    touch ${prefix}.agp
+    touch ${prefix}.stats
+
+    cat <<-END_VERSIONS > versions.yml
+        ragtag: \$(echo \$(ragtag.py -v | sed 's/v//'))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/ragtag/scaffold/meta.yml b/modules/nf-core/ragtag/scaffold/meta.yml
new file mode 100644
index 000000000000..62eb0e495406
--- /dev/null
+++ b/modules/nf-core/ragtag/scaffold/meta.yml
@@ -0,0 +1,106 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: ragtag_scaffold
+description: |
+  Scaffolding is the process of ordering and orienting draft assembly (query)
+  sequences into longer sequences. Gaps (stretches of "N" characters) are placed
+  between adjacent query sequences to indicate the presence of unknown sequence.
+  RagTag uses whole-genome alignments to a reference assembly to scaffold query sequences.
+  RagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.
+keywords:
+  - scaffolding
+  - ragtag
+  - assembly
+  - genome
+tools:
+  - "ragtag":
+      description: "Fast reference-guided genome assembly scaffolding"
+      homepage: "https://github.com/malonge/RagTag/wiki"
+      documentation: "https://github.com/malonge/RagTag/wiki"
+      tool_dev_url: "https://github.com/malonge/RagTag"
+      doi: "10.1186/s13059-022-02823-7"
+      licence: ["MIT"]
+      identifier: biotools:ragtag
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - assembly:
+        type: file
+        description: Assembly to be scaffolded
+        pattern: "*.{fasta,fasta.gz,fa,fa.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - reference:
+        type: file
+        description: Reference assembly
+        pattern: "*.{fasta,fasta.gz,fa,fa.gz}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - exclude:
+        type: file
+        description: list of target sequences to ignore
+        pattern: "*.txt"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - skip:
+        type: file
+        description: list of query sequences to leave unplaced
+        pattern: "*.txt"
+    - hard_skip:
+        type: file
+        description: list of query headers to leave unplaced and exclude from 'chr0'
+          ('-C')
+        pattern: "*.txt"
+output:
+  - corrected_assembly:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.fasta":
+          type: file
+          description: FASTA file containing the patched assembly
+          pattern: "*.fasta"
+  - corrected_agp:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.agp":
+          type: file
+          description: agp file defining how corrected_assembly is built
+          pattern: "*.agp"
+  - corrected_stats:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.stats":
+          type: file
+          description: Statistics on the scaffold
+          pattern: "*.stats"
+
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@nschan"
+maintainers:
+  - "@nschan"
diff --git a/modules/nf-core/ragtag/scaffold/tests/main.nf.test b/modules/nf-core/ragtag/scaffold/tests/main.nf.test
new file mode 100644
index 000000000000..51b42642510d
--- /dev/null
+++ b/modules/nf-core/ragtag/scaffold/tests/main.nf.test
@@ -0,0 +1,81 @@
+nextflow_process {
+
+    name "Test Process RAGTAG_SCAFFOLD"
+    script "../main.nf"
+    process "RAGTAG_SCAFFOLD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ragtag"
+    tag "ragtag/scaffold"
+
+    test("A. thaliana Col-0 test data - ragtag - scaffold") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[2] = [
+                    [],
+                    []
+                ]
+                input[3]  = [
+                    [],
+                    [],
+                    []
+                ]  
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+    test("A. thaliana Col-0 test data - ragtag - scaffold - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                input[2] = [
+                     [],
+                     []
+                ]
+                input[3]  = [
+                    [],
+                    [],
+                    []
+                ]  
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/ragtag/scaffold/tests/main.nf.test.snap b/modules/nf-core/ragtag/scaffold/tests/main.nf.test.snap
new file mode 100644
index 000000000000..e4faf0b0fe39
--- /dev/null
+++ b/modules/nf-core/ragtag/scaffold/tests/main.nf.test.snap
@@ -0,0 +1,132 @@
+{
+    "A. thaliana Col-0 test data - ragtag - scaffold": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,70b661fab5364a1c389972a771f97905"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agp:md5,40fbf2d081c32880d8ce8187c529a80b"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,209e973e4bac1653b8d5fddb7fa13b63"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,48710c1720f668d8ba3397f99892959e"
+                ],
+                "corrected_agp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agp:md5,40fbf2d081c32880d8ce8187c529a80b"
+                    ]
+                ],
+                "corrected_assembly": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,70b661fab5364a1c389972a771f97905"
+                    ]
+                ],
+                "corrected_stats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,209e973e4bac1653b8d5fddb7fa13b63"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,48710c1720f668d8ba3397f99892959e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-04T13:37:54.181644032"
+    },
+    "A. thaliana Col-0 test data - ragtag - scaffold - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,cecbb39907d607affa6522e395b78a1f"
+                ],
+                "corrected_agp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "corrected_assembly": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "corrected_stats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cecbb39907d607affa6522e395b78a1f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-04-04T13:38:21.635495713"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/tnhaplotyper2/main.nf b/modules/nf-core/sentieon/tnhaplotyper2/main.nf
index d1642a767c06..80b01a4883c4 100644
--- a/modules/nf-core/sentieon/tnhaplotyper2/main.nf
+++ b/modules/nf-core/sentieon/tnhaplotyper2/main.nf
@@ -58,7 +58,6 @@ process SENTIEON_TNHAPLOTYPER2 {
         ""
     """
     $sentieonLicense
-    export SENTIEON_LICENSE=${license}
 
     sentieon driver \\
         -t $task.cpus \\
diff --git a/modules/nf-core/sentieon/tnhaplotyper2/meta.yml b/modules/nf-core/sentieon/tnhaplotyper2/meta.yml
index d533b024d3c1..a8d0a58446d5 100644
--- a/modules/nf-core/sentieon/tnhaplotyper2/meta.yml
+++ b/modules/nf-core/sentieon/tnhaplotyper2/meta.yml
@@ -19,7 +19,7 @@ input:
         type: map
         description: |
           Groovy Map containing sample information.
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - input:
         type: file
         description: BAM/CRAM file(s) from alignment
diff --git a/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test b/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test
index 9358baa1c98f..87f3e29ed38c 100644
--- a/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test
+++ b/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test
@@ -9,8 +9,6 @@ nextflow_process {
     tag "modules_nfcore"
     tag "picard"
     tag "picard/addorreplacereadgroups"
-    tag "samtools"
-    tag "samtools/index"
     tag "sentieon"
     tag "sentieon/tnhaplotyper2"
     config './nextflow.config'
@@ -46,7 +44,7 @@ nextflow_process {
         }
     }
 
-    test("test_tnhaplotyper2_no_pon") {
+    test("no pon") {
 
         when {
             params {
@@ -65,9 +63,7 @@ nextflow_process {
                     meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
                     [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
                     }
-                input[1] = [[:],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)
-                    ]
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
                 input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
                 input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
                 input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
@@ -87,4 +83,276 @@ nextflow_process {
         }
     }
 
+    test("with pon") {
+
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join(NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
+                input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
+                input[5] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi',checkIfExists:true)]
+                input[6] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz',checkIfExists:true)]
+                input[7] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi',checkIfExists:true)]
+                input[8] = false
+                input[9] = false
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_tnhaplotyper2_emit_contamination_and_orientation_data") {
+
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = '--tumor_sample tumour'
+                module_args4 = '--tumor_sample tumour --normal_sample normal'
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join(NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
+                input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
+                input[5] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi',checkIfExists:true)]
+                input[6] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz',checkIfExists:true)]
+                input[7] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi',checkIfExists:true)]
+                input[8] = true
+                input[9] = true
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_tnhaplotyper2_no_normal") {
+
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour'
+                module_args3 = '--tumor_sample tumour'
+                module_args4 = '--tumor_sample tumour'
+            }
+            process {
+                """
+                input[0] = TUMOUR_ADDORREPLACEREADGROUPS.out.bam
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,tumour_bam,tumour_bai->
+                    [meta,tumour_bam,tumour_bai,[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
+                input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
+                input[5] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi',checkIfExists:true)]
+                input[6] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz',checkIfExists:true)]
+                input[7] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi',checkIfExists:true)]
+                input[8] = true
+                input[9] = true
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_tnhaplotyper2_no_pon -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join(NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
+                input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
+                input[5] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi',checkIfExists:true)]
+                input[6] = [[:],[]]
+                input[7] = [[:],[]]
+                input[8] = false
+                input[9] = false
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_tnhaplotyper2 -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join(NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
+                input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
+                input[5] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi',checkIfExists:true)]
+                input[6] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz',checkIfExists:true)]
+                input[7] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi',checkIfExists:true)]
+                input[8] = false
+                input[9] = false
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_tnhaplotyper2_emit_contamination_and_orientation_data -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join(NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
+                input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
+                input[5] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi',checkIfExists:true)]
+                input[6] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz',checkIfExists:true)]
+                input[7] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi',checkIfExists:true)]
+                input[8] = true
+                input[9] = true
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_tnhaplotyper2_no_normal -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = TUMOUR_ADDORREPLACEREADGROUPS.out.bam
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,tumour_bam,tumour_bai->
+                    [meta,tumour_bam,tumour_bai,[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict',checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta',checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai',checkIfExists:true)]
+                input[4] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz',checkIfExists:true)]
+                input[5] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi',checkIfExists:true)]
+                input[6] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz',checkIfExists:true)]
+                input[7] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi',checkIfExists:true)]
+                input[8] = true
+                input[9] = true
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test.snap b/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test.snap
index c76db4850f15..b6ce59162f92 100644
--- a/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test.snap
+++ b/modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test.snap
@@ -224,16 +224,31 @@
                     
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,9b9284beaf38e95b2ca1aaeb363f77f8"
+                    ]
                 ],
                 "4": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,2ad56cf9b300525f36682110d8fcf766"
+                    ]
                 ],
                 "5": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,fa322fb412a035087e950a00026545a4"
+                    ]
                 ],
                 "6": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ],
                 "contamination_data": [
                     
@@ -242,133 +257,268 @@
                     
                 ],
                 "index": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,fa322fb412a035087e950a00026545a4"
+                    ]
                 ],
                 "orientation_data": [
                     
                 ],
                 "stats": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,9b9284beaf38e95b2ca1aaeb363f77f8"
+                    ]
                 ],
                 "vcf": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,2ad56cf9b300525f36682110d8fcf766"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-04-01T15:33:02.550709028"
+        "timestamp": "2025-04-10T19:34:28.821280865"
     },
     "test_tnhaplotyper2_emit_contamination_and_orientation_data": {
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.orientation_data.tsv:md5,2f2ed6486c03bb1be674ccf905fcb6b3"
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contamination_data.tsv:md5,c8c5a8d53c3f1c48e26a7642b08dfcf2"
+                    ]
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.segments:md5,134a818bd0413185f068885391da05df"
+                    ]
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,9b9284beaf38e95b2ca1aaeb363f77f8"
+                    ]
                 ],
                 "4": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,de78f362256d0123acf03be904263c9f"
+                    ]
                 ],
                 "5": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,fa322fb412a035087e950a00026545a4"
+                    ]
                 ],
                 "6": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ],
                 "contamination_data": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contamination_data.tsv:md5,c8c5a8d53c3f1c48e26a7642b08dfcf2"
+                    ]
                 ],
                 "contamination_segments": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.segments:md5,134a818bd0413185f068885391da05df"
+                    ]
                 ],
                 "index": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,fa322fb412a035087e950a00026545a4"
+                    ]
                 ],
                 "orientation_data": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.orientation_data.tsv:md5,2f2ed6486c03bb1be674ccf905fcb6b3"
+                    ]
                 ],
                 "stats": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,9b9284beaf38e95b2ca1aaeb363f77f8"
+                    ]
                 ],
                 "vcf": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,de78f362256d0123acf03be904263c9f"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-04-01T15:33:20.031644999"
+        "timestamp": "2025-04-10T19:37:16.169623375"
     },
     "test_tnhaplotyper2_no_normal": {
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.orientation_data.tsv:md5,2f2ed6486c03bb1be674ccf905fcb6b3"
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contamination_data.tsv:md5,c8c5a8d53c3f1c48e26a7642b08dfcf2"
+                    ]
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.segments:md5,134a818bd0413185f068885391da05df"
+                    ]
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,e4d150874fe502a198c75f7398d1a55e"
+                    ]
                 ],
                 "4": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,af0e4bfb8d5867d68bfea629e4316aa0"
+                    ]
                 ],
                 "5": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,c1471146d73f140457611607ac00edbc"
+                    ]
                 ],
                 "6": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ],
                 "contamination_data": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contamination_data.tsv:md5,c8c5a8d53c3f1c48e26a7642b08dfcf2"
+                    ]
                 ],
                 "contamination_segments": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.segments:md5,134a818bd0413185f068885391da05df"
+                    ]
                 ],
                 "index": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,c1471146d73f140457611607ac00edbc"
+                    ]
                 ],
                 "orientation_data": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.orientation_data.tsv:md5,2f2ed6486c03bb1be674ccf905fcb6b3"
+                    ]
                 ],
                 "stats": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,e4d150874fe502a198c75f7398d1a55e"
+                    ]
                 ],
                 "vcf": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,af0e4bfb8d5867d68bfea629e4316aa0"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-04-01T15:33:37.788853048"
+        "timestamp": "2025-04-10T19:39:33.745325482"
     },
     "test_tnhaplotyper2_no_pon": {
         "content": [
@@ -383,16 +533,31 @@
                     
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,33493aaf38103a76df205f22d287b17d"
+                    ]
                 ],
                 "4": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,53b97cf19cd2850a812588930656f99b"
+                    ]
                 ],
                 "5": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,8349aaa3c14047f2dfd4b2ddd746ffb3"
+                    ]
                 ],
                 "6": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ],
                 "contamination_data": [
                     
@@ -401,26 +566,41 @@
                     
                 ],
                 "index": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,8349aaa3c14047f2dfd4b2ddd746ffb3"
+                    ]
                 ],
                 "orientation_data": [
                     
                 ],
                 "stats": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.stats:md5,33493aaf38103a76df205f22d287b17d"
+                    ]
                 ],
                 "vcf": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,53b97cf19cd2850a812588930656f99b"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,a2718daeef301a0740e6186bf6ba42e7"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-04-01T15:32:41.358068419"
+        "timestamp": "2025-04-10T19:31:51.711632084"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/tnhaplotyper2/tests/nextflow.config b/modules/nf-core/sentieon/tnhaplotyper2/tests/nextflow.config
index 999b8f1e35a7..c39a9b26ac62 100644
--- a/modules/nf-core/sentieon/tnhaplotyper2/tests/nextflow.config
+++ b/modules/nf-core/sentieon/tnhaplotyper2/tests/nextflow.config
@@ -18,3 +18,13 @@ process {
     }
 
 }
+
+env {
+    // NOTE This is how nf-core/sarek users will use Sentieon in real world use
+    SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP"
+    // NOTE This should only happen in GitHub actions or nf-core MegaTests
+    SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH"
+    SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA
+    // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file
+    // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
+}
diff --git a/modules/nf-core/sentieon/tnscope/main.nf b/modules/nf-core/sentieon/tnscope/main.nf
index 3cfd2f3953fa..ba992dfe784f 100644
--- a/modules/nf-core/sentieon/tnscope/main.nf
+++ b/modules/nf-core/sentieon/tnscope/main.nf
@@ -9,13 +9,15 @@ process SENTIEON_TNSCOPE {
         'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
-    tuple val(meta), path(input), path(input_index)
+    tuple val(meta), path(input), path(input_index), path(intervals)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
-    tuple val(meta4), path(cosmic), path(cosmic_tbi)
-    tuple val(meta5), path(pon)   , path(pon_tbi)
-    tuple val(meta6), path(dbsnp) , path(dbsnp_tbi)
-    tuple val(meta7), path(interval)
+    tuple val(meta4), path(dbsnp)
+    tuple val(meta5), path(dbsnp_tbi)
+    tuple val(meta6), path(pon)
+    tuple val(meta7), path(pon_tbi)
+    tuple val(meta8), path(cosmic)
+    tuple val(meta9), path(cosmic_tbi)
 
     output:
     tuple val(meta), path("*.vcf.gz")    , emit: vcf
@@ -28,7 +30,7 @@ process SENTIEON_TNSCOPE {
     script:
     def args         = task.ext.args     ?: ''
     def args2        = task.ext.args2    ?: ''
-    def interval_str = interval          ? "--interval ${interval}" : ''
+    def interval_str = intervals         ? "--interval ${interval}" : ''
     def cosmic_str   = cosmic            ? "--cosmic ${cosmic}"     : ''
     def dbsnp_str    = dbsnp             ? "--dbsnp ${dbsnp}"       : ''
     def pon_str      = pon               ? "--pon ${pon}"           : ''
@@ -47,7 +49,6 @@ process SENTIEON_TNSCOPE {
         $interval_str \\
         $args \\
         --algo TNscope \\
-        --tumor_sample ${meta.id} \\
         $args2 \\
         $cosmic_str \\
         $dbsnp_str \\
diff --git a/modules/nf-core/sentieon/tnscope/meta.yml b/modules/nf-core/sentieon/tnscope/meta.yml
index 36dcd8d8e688..e6a2d7e59c38 100644
--- a/modules/nf-core/sentieon/tnscope/meta.yml
+++ b/modules/nf-core/sentieon/tnscope/meta.yml
@@ -18,15 +18,21 @@ input:
         type: map
         description: |
           Groovy Map containing sample information.
-          e.g. [ id:'test', single_end:false ]
-    - bam:
+          e.g. [ id:'test' ]
+    - input:
+        type: file
+        description: One or more BAM or CRAM files.
+        pattern: "*.{bam,cram}"
+    - input_index:
         type: file
-        description: BAM file.
-        pattern: "*.bam"
-    - bai:
+        description: Indices for the input files
+        pattern: "*.{bai,crai}"
+    - intervals:
         type: file
-        description: BAI file
-        pattern: "*.bai"
+        description: bed or interval_list file containing interval in the reference
+          that will be used in the analysis. Only recommended for large WGS data, else 
+          the overhead may not be worth the additional parallelisation.
+        pattern: "*.{bed,interval_list}"
   - - meta2:
         type: map
         description: |
@@ -50,15 +56,20 @@ input:
         description: |
           Groovy Map containing reference information.
           e.g. [ id:'test' ]
-    - cosmic:
+    - dbsnp:
         type: file
         description: Single Nucleotide Polymorphism database (dbSNP) file
         pattern: "*.vcf.gz"
-    - cosmic_tbi:
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. [ id:'test' ]
+    - dbsnp_tbi:
         type: file
         description: Index of the Single Nucleotide Polymorphism database (dbSNP) file
         pattern: "*.vcf.gz.tbi"
-  - - meta5:
+  - - meta6:
         type: map
         description: |
           Groovy Map containing reference information.
@@ -67,40 +78,40 @@ input:
         type: file
         description: Single Nucleotide Polymorphism database (dbSNP) file
         pattern: "*.vcf.gz"
+  - - meta7:
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. [ id:'test' ]
     - pon_tbi:
         type: file
         description: Index of the Single Nucleotide Polymorphism database (dbSNP) file
         pattern: "*.vcf.gz.tbi"
-  - - meta6:
+  - - meta8:
         type: map
         description: |
           Groovy Map containing reference information.
           e.g. [ id:'test' ]
-    - dbsnp:
+    - cosmic:
         type: file
-        description: Single Nucleotide Polymorphism database (dbSNP) file
+        description: Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.
         pattern: "*.vcf.gz"
-    - dbsnp_tbi:
-        type: file
-        description: Index of the Single Nucleotide Polymorphism database (dbSNP) file
-        pattern: "*.vcf.gz.tbi"
-  - - meta7:
+  - - meta9:
         type: map
         description: |
           Groovy Map containing reference information.
           e.g. [ id:'test' ]
-    - interval:
+    - cosmic_tbi:
         type: file
-        description: bed or interval_list file containing interval in the reference
-          that will be used in the analysis
-        pattern: "*.{bed,interval_list}"
+        description: Index of the Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.
+        pattern: "*.vcf.gz.tbi"
 output:
   - vcf:
       - meta:
           type: map
           description: |
             Groovy Map containing reference information.
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*.vcf.gz":
           type: file
           description: VCF file
@@ -110,7 +121,7 @@ output:
           type: map
           description: |
             Groovy Map containing reference information.
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*.vcf.gz.tbi":
           type: file
           description: Index of the VCF file
diff --git a/modules/nf-core/sentieon/tnscope/tests/main.nf.test b/modules/nf-core/sentieon/tnscope/tests/main.nf.test
index d69cc71a8c0a..8e2c671d1b8e 100644
--- a/modules/nf-core/sentieon/tnscope/tests/main.nf.test
+++ b/modules/nf-core/sentieon/tnscope/tests/main.nf.test
@@ -11,11 +11,11 @@ nextflow_process {
     tag "picard/addorreplacereadgroups"
     tag "sentieon"
     tag "sentieon/tnscope"
+    config './nextflow.config'
 
     setup {
         run("PICARD_ADDORREPLACEREADGROUPS", alias: "NORMAL_ADDORREPLACEREADGROUPS") {
             script "../../../picard/addorreplacereadgroups/main.nf"
-            config './nextflow.config'
             process {
                 """
                 input[0] = [[id:'test'],// meta map
@@ -29,8 +29,6 @@ nextflow_process {
 
         run("PICARD_ADDORREPLACEREADGROUPS", alias: "TUMOUR_ADDORREPLACEREADGROUPS") {
             script "../../../picard/addorreplacereadgroups/main.nf"
-            config './nextflow.config'
-
             process {
                 """
                 input[0] = [[id:'test'],// meta map
@@ -43,9 +41,53 @@ nextflow_process {
         }
     }
 
-    test("test_tnscope") {
+    test("tumour normal - no dbsnp") {
+        
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join( NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join( TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join( TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'tumour'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [ [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists:true)
+                    ]
+                input[2] = [ [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists:true)
+                    ]
+                input[3] = [[:],[]]
+                input[4] = [[:],[]]
+                input[5] = [[:],[]]
+                input[6] = [[:],[]]
+                input[7] = [[:],[]]
+                input[8] = [[:],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("tumour normal - dbsnp") {
 
         when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+            }
             process {
                 """
                 input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
@@ -54,18 +96,27 @@ nextflow_process {
                     .join( TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
                     .map{
                     meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
-                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    [[id:'tumour'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
                     }
                 input[1] = [ [id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists:true)
                     ]
                 input[2] = [ [id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists:true)
                     ]
-                input[3] = [[:],[],[]]
-                input[4] = [[:],[],[]]
-                input[5] = [[:],[],[]]
+                input[3] = [
+                    [id:'dbsnp'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz',checkIfExists:true)
+                ]
+                input[4] = [
+                    [id:'dbsnp'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi',checkIfExists:true)
+                ]                
+                input[5] = [[:],[]]
                 input[6] = [[:],[]]
+                input[7] = [[:],[]]
+                input[8] = [[:],[]]
+
                 """
             }
         }
@@ -77,9 +128,13 @@ nextflow_process {
         }
     }
 
-    test("test_tnscope -- stub") {
+    test("tumour normal - no pon - stub") {
         options '-stub'
         when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+            }
             process {
                 """
                 input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
@@ -91,15 +146,17 @@ nextflow_process {
                     [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
                     }
                 input[1] = [ [id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists:true)
                     ]
                 input[2] = [ [id:'test'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists:true)
                     ]
-                input[3] = [[:],[],[]]
-                input[4] = [[:],[],[]]
-                input[5] = [[:],[],[]]
+                input[3] = [[:],[]]
+                input[4] = [[:],[]]
+                input[5] = [[:],[]]
                 input[6] = [[:],[]]
+                input[7] = [[:],[]]
+                input[8] = [[:],[]]
                 """
             }
         }
@@ -110,4 +167,5 @@ nextflow_process {
             )
         }
     }
+
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/tnscope/tests/main.nf.test.snap b/modules/nf-core/sentieon/tnscope/tests/main.nf.test.snap
index 8c9488e0fe9a..5feb222b7190 100644
--- a/modules/nf-core/sentieon/tnscope/tests/main.nf.test.snap
+++ b/modules/nf-core/sentieon/tnscope/tests/main.nf.test.snap
@@ -1,34 +1,54 @@
 {
-    "test_tnscope -- stub": {
+    "tumour normal - dbsnp": {
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz:md5,74242488a5624c56b4be27bace1191c6"
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz.tbi:md5,bdf38f0280dc5fb1c3b38ca267b0ee6c"
+                    ]
                 ],
                 "2": [
-                    
+                    "versions.yml:md5,6acc4c591fbca06fd1c34f2b20456fb7"
                 ],
                 "index": [
-                    
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz.tbi:md5,bdf38f0280dc5fb1c3b38ca267b0ee6c"
+                    ]
                 ],
                 "vcf": [
-                    
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz:md5,74242488a5624c56b4be27bace1191c6"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,6acc4c591fbca06fd1c34f2b20456fb7"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-04-08T12:55:05.902554475"
+        "timestamp": "2025-04-11T21:21:13.909876466"
     },
-    "test_tnscope": {
+    "tumour normal - no pon - stub": {
         "content": [
             {
                 "0": [
@@ -53,8 +73,57 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T21:22:01.486921036"
+    },
+    "tumour normal - no dbsnp": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz:md5,dd6056b23180902e82711efb1bf17be2"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz.tbi:md5,bdf38f0280dc5fb1c3b38ca267b0ee6c"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,6acc4c591fbca06fd1c34f2b20456fb7"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz.tbi:md5,bdf38f0280dc5fb1c3b38ca267b0ee6c"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "tumour"
+                        },
+                        "tumour.vcf.gz:md5,dd6056b23180902e82711efb1bf17be2"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6acc4c591fbca06fd1c34f2b20456fb7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-04-08T12:54:20.570572768"
+        "timestamp": "2025-04-11T21:19:45.340268715"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/tnscope/tests/nextflow.config b/modules/nf-core/sentieon/tnscope/tests/nextflow.config
index 330391c32dbd..ecf20e4e9369 100644
--- a/modules/nf-core/sentieon/tnscope/tests/nextflow.config
+++ b/modules/nf-core/sentieon/tnscope/tests/nextflow.config
@@ -10,4 +10,19 @@ process {
         ext.prefix = "normal"
     }
 
+    withName: 'SENTIEON_TNSCOPE' {
+        ext.args = params.module_args
+        ext.args2 = params.module_args2
+    }
+
+}
+
+env {
+    // NOTE This is how nf-core/sarek users will use Sentieon in real world use
+    SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP"
+    // NOTE This should only happen in GitHub actions or nf-core MegaTests
+    SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH"
+    SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA
+    // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file
+    // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
 }
diff --git a/modules/nf-core/seqkit/concat/main.nf b/modules/nf-core/seqkit/concat/main.nf
index d10d9780fb7f..748c96b5855e 100644
--- a/modules/nf-core/seqkit/concat/main.nf
+++ b/modules/nf-core/seqkit/concat/main.nf
@@ -1,30 +1,31 @@
 process SEQKIT_CONCAT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
-        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
+        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(input, stageAs: 'in/*')
 
     output:
     tuple val(meta), path("*.{fasta,fastq,fa,fq,fas,fna,faa}"), emit: fastx
-    path "versions.yml",                                        emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args        = task.ext.args         ?: ""
-    def prefix      = task.ext.prefix       ?: "${meta.id}"
-    def file_type   = input instanceof List ? input[0].getExtension() : input.getExtension()
+    def args = task.ext.args ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def file_type = input instanceof List ? input[0].getExtension() : input.getExtension()
     """
     seqkit \\
         concat \\
-        $args \\
+        --threads ${task.cpus} \\
+        ${args} \\
         in/* > ${prefix}.${file_type}
 
     cat <<-END_VERSIONS > versions.yml
@@ -34,7 +35,7 @@ process SEQKIT_CONCAT {
     """
 
     stub:
-    def prefix  = task.ext.prefix   ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.fasta
 
diff --git a/modules/nf-core/seqkit/seq/main.nf b/modules/nf-core/seqkit/seq/main.nf
index 9d76da213c03..c3b6cb560e5d 100644
--- a/modules/nf-core/seqkit/seq/main.nf
+++ b/modules/nf-core/seqkit/seq/main.nf
@@ -1,41 +1,43 @@
 process SEQKIT_SEQ {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
     // File IO can be a bottleneck. See: https://bioinf.shenwei.me/seqkit/usage/#parallelization-of-cpu-intensive-jobs
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
-        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
+        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(fastx)
 
     output:
-    tuple val(meta), path("${prefix}.*")    , emit: fastx
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("${prefix}.*"), emit: fastx
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args        = task.ext.args ?: ''
-    def args2       = task.ext.args2 ?: ''
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    def extension   = "fastq"
-    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
-        extension   = "fasta"
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = "fastq"
+    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
+        extension = "fasta"
+    }
+    extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
+    def call_gzip = extension.endsWith('.gz') ? "| gzip -c ${args2}" : ''
+    if ("${prefix}.${extension}" == "${fastx}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
     }
-    extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
-    def call_gzip   = extension.endsWith('.gz') ? "| gzip -c $args2" : ''
-    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     seqkit \\
         seq \\
-        --threads $task.cpus \\
-        $args \\
-        $fastx \\
-        $call_gzip \\
+        --threads ${task.cpus} \\
+        ${args} \\
+        ${fastx} \\
+        ${call_gzip} \\
         > ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
@@ -45,13 +47,15 @@ process SEQKIT_SEQ {
     """
 
     stub:
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    def extension   = "fastq"
-    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
-        extension   = "fasta"
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = "fastq"
+    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
+        extension = "fasta"
     }
     extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
-    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("${prefix}.${extension}" == "${fastx}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    }
     """
     touch ${prefix}.${extension}
 
diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf
index 57d95cfdc06a..f69fcb6698ae 100644
--- a/modules/nf-core/seqkit/stats/main.nf
+++ b/modules/nf-core/seqkit/stats/main.nf
@@ -1,18 +1,18 @@
 process SEQKIT_STATS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
-        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
+        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(reads)
 
     output:
     tuple val(meta), path("*.tsv"), emit: stats
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,8 +23,9 @@ process SEQKIT_STATS {
     """
     seqkit stats \\
         --tabular \\
-        $args \\
-        $reads > '${prefix}.tsv'
+        --threads ${task.cpus} \\
+        ${args} \\
+        ${reads} > '${prefix}.tsv'
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/seqkit/translate/main.nf b/modules/nf-core/seqkit/translate/main.nf
index 12e8c4a811ff..cdb174f27ca6 100644
--- a/modules/nf-core/seqkit/translate/main.nf
+++ b/modules/nf-core/seqkit/translate/main.nf
@@ -1,33 +1,35 @@
 process SEQKIT_TRANSLATE {
-    tag "$meta.id"
-    label 'process_single'
+    tag "${meta.id}"
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
-        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
+        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(fastx)
 
     output:
     tuple val(meta), path("${prefix}.*"), emit: fastx
-    path "versions.yml"                 , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args        = task.ext.args ?: ''
-    def args2       = task.ext.args2 ?: ''
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    def extension   = "fastq"
-    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
-        extension   = "fasta"
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = "fastq"
+    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
+        extension = "fasta"
+    }
+    extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
+    def call_gzip = extension.endsWith('.gz') ? "| gzip -c ${args2}" : ''
+    if ("${prefix}.${extension}" == "${fastx}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
     }
-    extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
-    def call_gzip   = extension.endsWith('.gz') ? "| gzip -c $args2" : ''
-    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     seqkit \\
         translate \\
@@ -44,13 +46,15 @@ process SEQKIT_TRANSLATE {
     """
 
     stub:
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    def extension   = "fastq"
-    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
-        extension   = "fasta"
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = "fastq"
+    if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
+        extension = "fasta"
     }
     extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
-    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("${prefix}.${extension}" == "${fastx}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    }
     """
     touch ${prefix}.${extension}
 
diff --git a/modules/nf-core/shigeifinder/environment.yml b/modules/nf-core/shigeifinder/environment.yml
index 778691f653a4..4c04dd78aea6 100644
--- a/modules/nf-core/shigeifinder/environment.yml
+++ b/modules/nf-core/shigeifinder/environment.yml
@@ -1,7 +1,7 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::shigeifinder=1.3.2
+  - bioconda::shigeifinder=1.3.5
+  - conda-forge::setuptools=78.1.0
diff --git a/modules/nf-core/shigeifinder/main.nf b/modules/nf-core/shigeifinder/main.nf
index 797684d717e0..28687bf737e9 100644
--- a/modules/nf-core/shigeifinder/main.nf
+++ b/modules/nf-core/shigeifinder/main.nf
@@ -4,8 +4,8 @@ process SHIGEIFINDER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/shigeifinder:1.3.2--pyhdfd78af_0':
-        'biocontainers/shigeifinder:1.3.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/shigeifinder:1.3.5--pyhdfd78af_0':
+        'biocontainers/shigeifinder:1.3.5--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(seqs)
@@ -20,7 +20,7 @@ process SHIGEIFINDER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.3.5' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     shigeifinder \\
         $args \\
@@ -28,6 +28,17 @@ process SHIGEIFINDER {
         -t $task.cpus \\
         -i $seqs
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        shigeifinder: $VERSION
+    END_VERSIONS
+    """
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.3.5' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.tsv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         shigeifinder: $VERSION
diff --git a/modules/nf-core/shigeifinder/tests/main.nf.test b/modules/nf-core/shigeifinder/tests/main.nf.test
new file mode 100644
index 000000000000..103593845ed7
--- /dev/null
+++ b/modules/nf-core/shigeifinder/tests/main.nf.test
@@ -0,0 +1,108 @@
+nextflow_process {
+
+    name "Test Process SHIGEIFINDER"
+    config "./nextflow.config"
+    script "../main.nf"
+    process "SHIGEIFINDER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shigeifinder"
+
+    test("fasta - sarscov2") {
+
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    test("fastq - sarscov2") {
+
+        when {
+            params {
+                module_args = '-r '
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists:true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists:true)]
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fasta - sarscov2 -stub") {
+
+        options '-stub'
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    test("fastq - sarscov2 - stub") {
+
+        options '-stub'
+        when {
+            params {
+                module_args = '-r '
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists:true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists:true)]
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/shigeifinder/tests/main.nf.test.snap b/modules/nf-core/shigeifinder/tests/main.nf.test.snap
new file mode 100644
index 000000000000..ae397ab513f3
--- /dev/null
+++ b/modules/nf-core/shigeifinder/tests/main.nf.test.snap
@@ -0,0 +1,134 @@
+{
+    "fastq - sarscov2 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:39:16.152360715"
+    },
+    "fasta - sarscov2 -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:39:06.083372883"
+    },
+    "fasta - sarscov2": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,b9b0837765b574c4c61e14d1e90179cc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,b9b0837765b574c4c61e14d1e90179cc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:36:58.646944634"
+    },
+    "fastq - sarscov2": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,8f7f7db057d9c53abaa4c647532433ed"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,8f7f7db057d9c53abaa4c647532433ed"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,db972cf613541d0fe186986346dd85ab"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:37:09.244210737"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/shigeifinder/tests/nextflow.config b/modules/nf-core/shigeifinder/tests/nextflow.config
new file mode 100644
index 000000000000..59cf00a9f2ca
--- /dev/null
+++ b/modules/nf-core/shigeifinder/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "SHIGEIFINDER" {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml
index 27e26de95e7d..628cd2e65a8e 100644
--- a/modules/nf-core/shinyngs/app/environment.yml
+++ b/modules/nf-core/shinyngs/app/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.0
+  - bioconda::r-shinyngs=2.2.2
diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf
index 1305be0a9637..50c2f9747d44 100644
--- a/modules/nf-core/shinyngs/app/main.nf
+++ b/modules/nf-core/shinyngs/app/main.nf
@@ -1,4 +1,3 @@
-
 process SHINYNGS_APP {
     tag "$meta.id"
     label 'process_single'
@@ -15,8 +14,8 @@ process SHINYNGS_APP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78a62fc76571e1f1b6d3436967bef94de96f42107c7455ac10e2405bf228906c/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.0--d3069f31a8b211d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b0b2383d86ddb37ad7c2b8bc3c373926e8bc0cd08b137f457756c39e1589dd0/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.2.2--09ebd939fb477d18' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)    // Experiment-level info
diff --git a/modules/nf-core/shinyngs/app/tests/main.nf.test.snap b/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
index 21e4ba0351c2..5685434f135f 100644
--- a/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
@@ -4,41 +4,41 @@
             "data.rds",
             "app.R:md5,d41d8cd98f00b204e9800998ecf8427e",
             [
-                "versions.yml:md5,6f86c6ef85cf324515af09d1f6f6d92c"
+                "versions.yml:md5,5051415e8b0625cff043d5f1959767f0"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:41:20.444995"
+        "timestamp": "2025-04-02T10:16:55.630011"
     },
     "mouse - multi matrix": {
         "content": [
             "data.rds",
             "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
             [
-                "versions.yml:md5,6f86c6ef85cf324515af09d1f6f6d92c"
+                "versions.yml:md5,5051415e8b0625cff043d5f1959767f0"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:40:44.814087"
+        "timestamp": "2025-04-02T10:16:19.849024"
     },
     "mouse - single matrix": {
         "content": [
             "data.rds",
             "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
             [
-                "versions.yml:md5,6f86c6ef85cf324515af09d1f6f6d92c"
+                "versions.yml:md5,5051415e8b0625cff043d5f1959767f0"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:41:05.232494"
+        "timestamp": "2025-04-02T10:16:40.393736"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml
index 27e26de95e7d..628cd2e65a8e 100644
--- a/modules/nf-core/shinyngs/staticdifferential/environment.yml
+++ b/modules/nf-core/shinyngs/staticdifferential/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.0
+  - bioconda::r-shinyngs=2.2.2
diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf
index 3e4f10ebe4fd..02181241c2c7 100644
--- a/modules/nf-core/shinyngs/staticdifferential/main.nf
+++ b/modules/nf-core/shinyngs/staticdifferential/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICDIFFERENTIAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78a62fc76571e1f1b6d3436967bef94de96f42107c7455ac10e2405bf228906c/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.0--d3069f31a8b211d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b0b2383d86ddb37ad7c2b8bc3c373926e8bc0cd08b137f457756c39e1589dd0/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.2.2--09ebd939fb477d18' }"
 
     input:
     tuple val(meta), path(differential_result)                              // Differential info: contrast and differential stats
diff --git a/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap b/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap
index e1e5191f2a44..37a142e8d790 100644
--- a/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap
@@ -6,14 +6,14 @@
                 
             ],
             [
-                "versions.yml:md5,3cb47be8fd3c945b1dfb0e547b4b6b59"
+                "versions.yml:md5,0bac3f7d028b5eda56f8a4950c332ae9"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:56:38.833474"
+        "timestamp": "2025-04-02T10:19:23.562288"
     },
     "stub": {
         "content": [
@@ -43,10 +43,10 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,3cb47be8fd3c945b1dfb0e547b4b6b59"
+                    "versions.yml:md5,0bac3f7d028b5eda56f8a4950c332ae9"
                 ],
                 "versions": [
-                    "versions.yml:md5,3cb47be8fd3c945b1dfb0e547b4b6b59"
+                    "versions.yml:md5,0bac3f7d028b5eda56f8a4950c332ae9"
                 ],
                 "volcanos_html": [
                     [
@@ -78,6 +78,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:56:55.859629"
+        "timestamp": "2025-04-02T10:19:40.399781"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml
index 27e26de95e7d..628cd2e65a8e 100644
--- a/modules/nf-core/shinyngs/staticexploratory/environment.yml
+++ b/modules/nf-core/shinyngs/staticexploratory/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.0
+  - bioconda::r-shinyngs=2.2.2
diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf
index 78163d741ece..068633082848 100644
--- a/modules/nf-core/shinyngs/staticexploratory/main.nf
+++ b/modules/nf-core/shinyngs/staticexploratory/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICEXPLORATORY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78a62fc76571e1f1b6d3436967bef94de96f42107c7455ac10e2405bf228906c/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.0--d3069f31a8b211d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b0b2383d86ddb37ad7c2b8bc3c373926e8bc0cd08b137f457756c39e1589dd0/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.2.2--09ebd939fb477d18' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
index 15b466c68984..61d7ad79695d 100644
--- a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
@@ -8,14 +8,14 @@
             "pca3d.png",
             "sample_dendrogram.png",
             [
-                "versions.yml:md5,3f22225357b83bcaf3ef53d52886dced"
+                "versions.yml:md5,0085c0d839c6713a79a6089b273b7b2c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:52:20.835999"
+        "timestamp": "2025-04-02T10:20:37.364761"
     },
     "mouse - defaults": {
         "content": [
@@ -26,14 +26,14 @@
             "pca3d.png",
             "sample_dendrogram.png",
             [
-                "versions.yml:md5,3f22225357b83bcaf3ef53d52886dced"
+                "versions.yml:md5,0085c0d839c6713a79a6089b273b7b2c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:52:05.655984"
+        "timestamp": "2025-04-02T10:20:22.636752"
     },
     "mouse - specify log": {
         "content": [
@@ -44,14 +44,14 @@
             "pca3d.png",
             "sample_dendrogram.png",
             [
-                "versions.yml:md5,3f22225357b83bcaf3ef53d52886dced"
+                "versions.yml:md5,0085c0d839c6713a79a6089b273b7b2c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:52:42.334106"
+        "timestamp": "2025-04-02T10:20:58.524022"
     },
     "mouse - html": {
         "content": [
@@ -67,13 +67,13 @@
             false,
             false,
             [
-                "versions.yml:md5,3f22225357b83bcaf3ef53d52886dced"
+                "versions.yml:md5,0085c0d839c6713a79a6089b273b7b2c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:53:06.732642"
+        "timestamp": "2025-04-02T10:21:22.591369"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
index 27e26de95e7d..628cd2e65a8e 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
+++ b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.0
+  - bioconda::r-shinyngs=2.2.2
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
index 6a0eea82d0b1..2080624ef3a2 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/main.nf
+++ b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78a62fc76571e1f1b6d3436967bef94de96f42107c7455ac10e2405bf228906c/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.0--d3069f31a8b211d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b0b2383d86ddb37ad7c2b8bc3c373926e8bc0cd08b137f457756c39e1589dd0/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.2.2--09ebd939fb477d18' }"
 
     input:
     tuple val(meta),  path(sample), path(assay_files)
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap
index 12ffcce8f0d3..16d86819a788 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,96086209610243a193df68ad4baa2464"
+                    "versions.yml:md5,23a1a6e8316311b9578a85ed0d5a90ef"
                 ],
                 "assays": [
                     [
@@ -70,7 +70,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,96086209610243a193df68ad4baa2464"
+                    "versions.yml:md5,23a1a6e8316311b9578a85ed0d5a90ef"
                 ]
             }
         ],
@@ -78,7 +78,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:50:33.071241"
+        "timestamp": "2025-04-02T10:17:43.209812"
     },
     "stub": {
         "content": [
@@ -116,7 +116,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,96086209610243a193df68ad4baa2464"
+                    "versions.yml:md5,23a1a6e8316311b9578a85ed0d5a90ef"
                 ],
                 "assays": [
                     [
@@ -151,7 +151,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,96086209610243a193df68ad4baa2464"
+                    "versions.yml:md5,23a1a6e8316311b9578a85ed0d5a90ef"
                 ]
             }
         ],
@@ -159,7 +159,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:51:14.962119"
+        "timestamp": "2025-04-02T10:18:23.989692"
     },
     "test_yaml": {
         "content": [
@@ -193,11 +193,11 @@
                         {
                             "id": "SRP254919"
                         },
-                        "SRP254919.contrasts.contrasts_file.tsv:md5,e0980240404f48216aedb63b5094029f"
+                        "SRP254919.contrasts.contrasts_file.tsv:md5,4eab81efe03ce7a59dbce0db4015cf8d"
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,96086209610243a193df68ad4baa2464"
+                    "versions.yml:md5,23a1a6e8316311b9578a85ed0d5a90ef"
                 ],
                 "assays": [
                     [
@@ -212,7 +212,7 @@
                         {
                             "id": "SRP254919"
                         },
-                        "SRP254919.contrasts.contrasts_file.tsv:md5,e0980240404f48216aedb63b5094029f"
+                        "SRP254919.contrasts.contrasts_file.tsv:md5,4eab81efe03ce7a59dbce0db4015cf8d"
                     ]
                 ],
                 "feature_meta": [
@@ -232,7 +232,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,96086209610243a193df68ad4baa2464"
+                    "versions.yml:md5,23a1a6e8316311b9578a85ed0d5a90ef"
                 ]
             }
         ],
@@ -240,6 +240,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2025-02-27T16:50:57.612433"
+        "timestamp": "2025-04-02T10:18:07.403921"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/spaceranger/Dockerfile b/modules/nf-core/spaceranger/Dockerfile
index c08c4c14dd9b..d0a5b0126672 100644
--- a/modules/nf-core/spaceranger/Dockerfile
+++ b/modules/nf-core/spaceranger/Dockerfile
@@ -1,10 +1,10 @@
 # syntax=docker/dockerfile:1
 
-FROM mambaorg/micromamba:1.5.10-noble
-ARG SPACERANGER_VER="3.1.2"
+FROM mambaorg/micromamba:1.5.10-jammy
+ARG SPACERANGER_VER="3.1.3"
 # NOTE you need to go fill out the form to get a new download link
-ARG SPACERANGER_URL="https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-3.1.2.tar.gz?Expires=1732608367&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=S4jcGCs5H0wLFfREhSc~AfuPIOXE~PW96kX9o2EyxZnmn1goUecgfEWTj67fL1DnZJBIa06kFdUdNpsMn2ustiSWOfXEgjlYQnxIcNnQIiEBGoQTHWphvx3LEQ6wtZnkWS80P6IcE0HJkIsgy04t6Sohih5cxY4jgytYsrAfZDYr5G3KKFwTfCKmhzMaXqW635yPbyQ8xEcQHK0QwviAx8-EFq-PE8UzC4QgUKi2MW-ivcfZkSDSfF8C3s7SgwDXIGIWv52mzeszenxMjN4KrWQotZ7ZpktzI0Vfpz0dNC17dQeDQUHj4LuNYbdh3RqsPKtqu3wjCe2Q7KiyoWnmaw__" \"
-ARG SPACERANGER_SHA256="2566b24f29829b39f3add112a674990b1c54ae2fbe7ccb50a4c7dce9ccf152e6"
+ARG SPACERANGER_URL="https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-3.1.3.tar.gz?Expires=1739251752&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=ohLEz5jR~HNzWrUz4pd35VGlJP~g7ywmVDaD29BoCdUvio46HWEfhIuUT19D~2JoFlYsbaLQ2d~qIuBB-d9WmX9bdmoQ1vzc9ozikwufXhuJhvrvxIXAZ4kUreoGWX7b51emM7nq8kJxTL9CmTKQZXRe~DuQjP6q6z0XxDUxeLhdPRg3ACfj~jFgMlNfwiJwBRHDH3yM5Hrtz~gNmxZ9O0fl~KNwlzZh7Mtm9GG-GyXYOtM5KAPQjv69JpM2XiZoZFpaVbPq5uqGfr~B3GC1dY25MGqVgXavc~uQFVcsZiyF5BewbeFzYTKu0SiW4WdO21K5L6CdkJ1M5AflXZmpsw__" \"
+ARG SPACERANGER_SHA256="cee7e94942cf72af76e28ead0024992642f81f10b89006bf93756c1e08528522"
 LABEL org.opencontainers.image.authors="Gisela Gabernet <gisela.gabernet@gmail.com>,Edmund Miller <edmund@nf-co.re>"
 LABEL org.opencontainers.image.description="Docker image containing spaceranger"
 LABEL org.opencontainers.image.version="$SPACERANGER_VER"
diff --git a/modules/nf-core/spaceranger/README.md b/modules/nf-core/spaceranger/README.md
index 3fb4113f2798..b6cab83efc89 100644
--- a/modules/nf-core/spaceranger/README.md
+++ b/modules/nf-core/spaceranger/README.md
@@ -15,4 +15,4 @@ Space Ranger is a commercial tool by 10X Genomics. The container provided for th
 + ARG SPACERANGER_SHA256="<Manual SHA256 of tar.gz>"
 ```
 
-3. Push the changes and the Dockerfile should be built and uploaded to `quay.io/nf-core/modules/spaceranger`!
+3. Push the changes and the Dockerfile should be built and uploaded to `quay.io/nf-core/spaceranger`!
diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf
index f33d82fcc7ea..6d882b233cd2 100644
--- a/modules/nf-core/spaceranger/count/main.nf
+++ b/modules/nf-core/spaceranger/count/main.nf
@@ -2,10 +2,10 @@ process SPACERANGER_COUNT {
     tag "$meta.id"
     label 'process_high'
 
-    container "nf-core/modules/spaceranger:d71611e316a8614b"
+    container "nf-core/spaceranger:3.1.3"
 
     input:
-    tuple val(meta), path(reads), path(image), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile)
+    tuple val(meta), path(reads), path(image), val(slide), val(area), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile)
     path(reference)
     path(probeset)
 
@@ -31,17 +31,21 @@ process SPACERANGER_COUNT {
     def cytaimage = cytaimage ? "--cytaimage=\"${cytaimage}\"" : ""
     def darkimage = darkimage ? "--darkimage=\"${darkimage}\"" : ""
     def colorizedimage = colorizedimage ? "--colorizedimage=\"${colorizedimage}\"" : ""
+    if (slide.matches("visium-(.*)") && area == "" && slidefile == "") {
+        slide_and_area = "--unknown-slide=\"${slide}\""
+    } else {
+        slide_and_area = "--slide=\"${slide}\" --area=\"${area}\""
+    }
     """
     spaceranger count \\
         --id="${prefix}" \\
         --sample="${meta.id}" \\
         --fastqs=. \\
-        --slide="${meta.slide}" \\
-        --area="${meta.area}" \\
         --transcriptome="${reference}" \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
         $image $cytaimage $darkimage $colorizedimage \\
+        $slide_and_area \\
         $probeset \\
         $alignment \\
         $slidefile \\
diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml
index e1ffcefc9daa..8be997270d1b 100644
--- a/modules/nf-core/spaceranger/count/meta.yml
+++ b/modules/nf-core/spaceranger/count/meta.yml
@@ -41,6 +41,12 @@ input:
         type: file
         description: Brightfield tissue H&E image in JPEG or TIFF format.
         pattern: "*.{tif,tiff,jpg,jpeg}"
+    - slide:
+        type: string
+        description: Visium slide ID used for the sample.
+    - area:
+        type: string
+        description: Visium slide capture area used for the sample.
     - cytaimage:
         type: file
         description: |
diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test b/modules/nf-core/spaceranger/count/tests/main.nf.test
index 49a9d5f69c9d..3d65e686ee6f 100644
--- a/modules/nf-core/spaceranger/count/tests/main.nf.test
+++ b/modules/nf-core/spaceranger/count/tests/main.nf.test
@@ -43,15 +43,15 @@ nextflow_process {
                 """
                 input[0] = [
                     [
-                        id: 'Visium_FFPE_Human_Ovarian_Cancer',
-                        slide: 'V10L13-020',
-                        area: 'D1'
+                        id: 'Visium_FFPE_Human_Ovarian_Cancer'
                     ], // Meta map
                     [
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz', checkIfExists: true),
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz', checkIfExists: true)
                     ], // Reads
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg', checkIfExists: true), // Image
+                    'V10L13-020', // Slide
+                    'D1', // Area
                     [], // Cytaimage
                     [], // Darkimage
                     [], // Colorizedimage
@@ -68,7 +68,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    path(process.out.versions.get(0)).yaml,
+                    process.out.versions,
                     process.out.outs.get(0).get(1).findAll { file(it).name !in [
                         'web_summary.html',
                         'scalefactors_json.json',
@@ -120,15 +120,15 @@ nextflow_process {
                 """
                 input[0] = [
                     [
-                        id: 'Visium_FFPE_Human_Ovarian_Cancer',
-                        slide: 'V10L13-020',
-                        area: 'D1'
+                        id: 'Visium_FFPE_Human_Ovarian_Cancer'
                     ], // Meta map
                     [
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz', checkIfExists: true),
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz', checkIfExists: true)
                     ], // Reads
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg', checkIfExists: true), // Image
+                    'V10L13-020', // Slide
+                    'D1', // Area
                     [], // Cytaimage
                     [], // Darkimage
                     [], // Colorizedimage
@@ -144,7 +144,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
+                { assert snapshot(process.out.versions).match() },
             )
         }
     }
@@ -179,15 +179,15 @@ nextflow_process {
                 """
                 input[0] = [
                     [
-                        id: 'CytAssist_11mm_FFPE_Human_Glioblastoma_2',
-                        slide: 'V52Y10-317',
-                        area: 'B1'
+                        id: 'CytAssist_11mm_FFPE_Human_Glioblastoma_2'
                     ], // Meta map
                     [
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz', checkIfExists: true),
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz', checkIfExists: true)
                     ], // Reads
                     [], // Image
+                    'V52Y10-317', // Slide
+                    'B1', // Area
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif', checkIfExists: true), // Cytaimage
                     [], // Darkimage
                     [], // Colorizedimage
@@ -204,7 +204,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    path(process.out.versions.get(0)).yaml,
+                    process.out.versions,
                     process.out.outs.get(0).get(1).findAll { file(it).name !in [
                         'web_summary.html',
                         'scalefactors_json.json',
diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test.snap b/modules/nf-core/spaceranger/count/tests/main.nf.test.snap
index 7a49d4545263..dbfaadf09696 100644
--- a/modules/nf-core/spaceranger/count/tests/main.nf.test.snap
+++ b/modules/nf-core/spaceranger/count/tests/main.nf.test.snap
@@ -1,25 +1,21 @@
 {
     "spaceranger v1 (stub) - homo_sapiens - fasta - gtf - fastq - tif - csv": {
         "content": [
-            {
-                "SPACERANGER_COUNT": {
-                    "spaceranger": "3.1.2"
-                }
-            }
+            [
+                "versions.yml:md5,4abe169f33d7f99d5d9876b189060aae"
+            ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-26T01:48:31.348979531"
+        "timestamp": "2025-02-13T09:02:47.710975472"
     },
     "spaceranger v2 - homo_sapiens - fasta - gtf - fastq - tif - csv": {
         "content": [
-            {
-                "SPACERANGER_COUNT": {
-                    "spaceranger": "3.1.2"
-                }
-            },
+            [
+                "versions.yml:md5,4abe169f33d7f99d5d9876b189060aae"
+            ],
             [
                 "clusters.csv:md5,221a4554e62ea94b0df8dbf637d2c13c",
                 "clusters.csv:md5,53ee76645943b5562392aac51d2d9f3f",
@@ -48,10 +44,10 @@
                 "variance.csv:md5,4159711ab5d64e97737fad9d75d945b3",
                 "projection.csv:md5,ce729f7e237df4570ac3e4a79251df24",
                 "projection.csv:md5,fa7bdefa8424b233fe6461129ab76d57",
-                "filtered_feature_bc_matrix.h5:md5,f625d7e2c063c8c079ccc35a853b356d",
+                "filtered_feature_bc_matrix.h5:md5,704256e5150522d9cf2e75e7e47221b6",
                 "metrics_summary.csv:md5,5ece84f5f8e08839749b1c8f2bff6701",
                 "probe_set.csv:md5,5bfb8f12319be1b2b6c14142537c3804",
-                "raw_feature_bc_matrix.h5:md5,90575715eb252f0b652c9d36a1f5628e",
+                "raw_feature_bc_matrix.h5:md5,ac24486662643ea68562c1a51cbbb2bd",
                 "raw_probe_bc_matrix.h5:md5,8ab08437814506f98e3f10107cfc38ac",
                 "aligned_fiducials.jpg:md5,51dcc3a32d3d5ca4704f664c8ede81ef",
                 "cytassist_image.tiff:md5,0fb04a55e5658f4d158d986a334b034d",
@@ -63,23 +59,21 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-26T01:58:16.555517048"
+        "timestamp": "2025-02-12T11:24:51.984883864"
     },
     "spaceranger v1 - homo_sapiens - fasta - gtf - fastq - tif - csv": {
         "content": [
-            {
-                "SPACERANGER_COUNT": {
-                    "spaceranger": "3.1.2"
-                }
-            },
             [
-                "filtered_feature_bc_matrix.h5:md5,a756f6dda550f52f9fb3e347207a2c6c",
+                "versions.yml:md5,4abe169f33d7f99d5d9876b189060aae"
+            ],
+            [
+                "filtered_feature_bc_matrix.h5:md5,649ac955bcb372b0b767013071cca72c",
                 "metrics_summary.csv:md5,38774fc5f54873d711b4898a2dd50e72",
-                "molecule_info.h5:md5,9e6393dbbccdfe58edf9e92181261f88",
-                "raw_feature_bc_matrix.h5:md5,860702876f936f89fdcec2b5f599a7d2",
+                "molecule_info.h5:md5,88bb948a426041165b2cc5fe8b180c21",
+                "raw_feature_bc_matrix.h5:md5,63324ae38fbf28bcc2114f170e0fde5d",
                 "aligned_fiducials.jpg:md5,f6217ddd707bb189e665f56b130c3da8",
                 "detected_tissue_image.jpg:md5,c1c7e8741701a576c1ec103c1aaf98ea",
                 "tissue_hires_image.png:md5,d91f8f176ae35ab824ede87117ac0889",
@@ -88,9 +82,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-26T01:48:13.569651476"
+        "timestamp": "2025-02-12T11:08:30.165324139"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/spaceranger/mkgtf/main.nf b/modules/nf-core/spaceranger/mkgtf/main.nf
index 7339b6a42a52..86e05cc77f7f 100644
--- a/modules/nf-core/spaceranger/mkgtf/main.nf
+++ b/modules/nf-core/spaceranger/mkgtf/main.nf
@@ -2,7 +2,7 @@ process SPACERANGER_MKGTF {
     tag "$gtf"
     label 'process_low'
 
-    container "nf-core/modules/spaceranger:d71611e316a8614b"
+    container "nf-core/spaceranger:3.1.3"
 
     input:
     path gtf
@@ -33,4 +33,19 @@ process SPACERANGER_MKGTF {
         spaceranger: \$(spaceranger -V | sed -e "s/spaceranger spaceranger-//g")
     END_VERSIONS
     """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "SPACERANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def prefix = task.ext.prefix ?: "${gtf.baseName}.filtered"
+    """
+    touch ${prefix}.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        spaceranger: \$(spaceranger -V | sed -e "s/spaceranger spaceranger-//g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test
index 626f5b5ef261..7091e0a09e64 100644
--- a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test
+++ b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test
@@ -26,11 +26,34 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.gtf,
-                    path(process.out.versions.get(0)).yaml,
+                    process.out.versions,
                 ).match() }
             )
         }
 
     }
 
+    test("homo_sapiens (stub) - gtf") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+            )
+        }
+
+    }
+
 }
\ No newline at end of file
diff --git a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test.snap b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test.snap
index 6b65a7027340..138a73908d0c 100644
--- a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test.snap
+++ b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test.snap
@@ -4,16 +4,26 @@
             [
                 "genome.filtered.gtf:md5,50fc877b1c53b36b3b413aff88bda48c"
             ],
-            {
-                "SPACERANGER_MKGTF": {
-                    "spaceranger": "3.1.2"
-                }
-            }
+            [
+                "versions.yml:md5,2f6c2b1181d43aea5c3fd8095cb181b6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-12T16:06:15.384050292"
+    },
+    "homo_sapiens (stub) - gtf": {
+        "content": [
+            [
+                "versions.yml:md5,2f6c2b1181d43aea5c3fd8095cb181b6"
+            ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-26T01:58:29.469616437"
+        "timestamp": "2025-02-12T16:43:38.384121778"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/spaceranger/mkref/main.nf b/modules/nf-core/spaceranger/mkref/main.nf
index 0646fa514f2e..824268da61b5 100644
--- a/modules/nf-core/spaceranger/mkref/main.nf
+++ b/modules/nf-core/spaceranger/mkref/main.nf
@@ -2,7 +2,7 @@ process SPACERANGER_MKREF {
     tag "$fasta"
     label 'process_high'
 
-    container "nf-core/modules/spaceranger:d71611e316a8614b"
+    container "nf-core/spaceranger:3.1.3"
 
     input:
     path fasta
diff --git a/modules/nf-core/spaceranger/mkref/tests/main.nf.test b/modules/nf-core/spaceranger/mkref/tests/main.nf.test
index a16da76afa0a..39b1547f88ae 100644
--- a/modules/nf-core/spaceranger/mkref/tests/main.nf.test
+++ b/modules/nf-core/spaceranger/mkref/tests/main.nf.test
@@ -25,7 +25,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    path(process.out.versions.get(0)).yaml,
+                    process.out.versions,
                     "${process.out.reference[0]}/fasta",
                     "${process.out.reference[0]}/genes",
                     "${process.out.reference[0]}/reference.json",
@@ -37,4 +37,27 @@ nextflow_process {
 
     }
 
+    test("homo_sapiens (stub) - fasta - gtf") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[2] = 'homo_sapiens_chr22_reference'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+            )
+        }
+
+    }
+
 }
\ No newline at end of file
diff --git a/modules/nf-core/spaceranger/mkref/tests/main.nf.test.snap b/modules/nf-core/spaceranger/mkref/tests/main.nf.test.snap
index 0801cc4694e4..dab7acf1c05d 100644
--- a/modules/nf-core/spaceranger/mkref/tests/main.nf.test.snap
+++ b/modules/nf-core/spaceranger/mkref/tests/main.nf.test.snap
@@ -1,11 +1,17 @@
 {
+    "homo_sapiens (stub) - fasta - gtf": {
+        "content": [
+            [
+                "versions.yml:md5,c18b9ac3b0bb942d0a164bfe184cce52"
+            ]
+        ],
+        "timestamp": "2025-02-24T15:36:16.846289"
+    },
     "homo_sapiens - fasta - gtf": {
         "content": [
-            {
-                "SPACERANGER_MKREF": {
-                    "spaceranger": "3.1.2"
-                }
-            },
+            [
+                "versions.yml:md5,c18b9ac3b0bb942d0a164bfe184cce52"
+            ],
             [
                 "genome.fa:md5,f315020d899597c1b57e5fe9f60f4c3e",
                 "genome.fa.fai:md5,3520cd30e1b100e55f578db9c855f685"
@@ -13,7 +19,7 @@
             [
                 "genes.gtf.gz:md5,50fc877b1c53b36b3b413aff88bda48c"
             ],
-            "reference.json:md5,fa6ca32036814b883644e323706bd247",
+            "reference.json:md5,08c5809af98db0cda9942720084599dd",
             [
                 "Genome:md5,22102926fadf5890e905ca71b2da3f35",
                 "SA:md5,bcf3e1a855783105150b46c905465333",
@@ -31,10 +37,6 @@
                 "transcriptInfo.tab:md5,0c3a5adb49d15e5feff81db8e29f2e36"
             ]
         ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
-        },
-        "timestamp": "2024-11-26T01:58:49.663386635"
+        "timestamp": "2025-02-24T15:35:49.747476"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/stecfinder/environment.yml b/modules/nf-core/stecfinder/environment.yml
index 4451180691f2..e56d1353b9cc 100644
--- a/modules/nf-core/stecfinder/environment.yml
+++ b/modules/nf-core/stecfinder/environment.yml
@@ -1,7 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::stecfinder=1.1.0
+  - bioconda::stecfinder=1.1.2
diff --git a/modules/nf-core/stecfinder/main.nf b/modules/nf-core/stecfinder/main.nf
index e145bc94d69c..9f1115148138 100644
--- a/modules/nf-core/stecfinder/main.nf
+++ b/modules/nf-core/stecfinder/main.nf
@@ -4,8 +4,8 @@ process STECFINDER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stecfinder:1.1.0--pyhdfd78af_0':
-        'biocontainers/stecfinder:1.1.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/stecfinder:1.1.2--pyhdfd78af_0':
+        'biocontainers/stecfinder:1.1.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(seqs)
@@ -31,4 +31,16 @@ process STECFINDER {
         stecfinder: \$(echo \$(stecfinder --version 2>&1) | sed 's/^.*STECFinder version: //;' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        stecfinder: \$(echo \$(stecfinder --version 2>&1) | sed 's/^.*STECFinder version: //;' )
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/stecfinder/tests/main.nf.test b/modules/nf-core/stecfinder/tests/main.nf.test
new file mode 100644
index 000000000000..18651b9c39f7
--- /dev/null
+++ b/modules/nf-core/stecfinder/tests/main.nf.test
@@ -0,0 +1,108 @@
+nextflow_process {
+
+    name "Test Process STECFINDER"
+    config "./nextflow.config"
+    script "../main.nf"
+    process "STECFINDER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "stecfinder"
+
+    test("fasta - sarscov2") {
+
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [[ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fastq - sarscov2") {
+
+        when {
+            params {
+                module_args = '-r'
+            }
+            process {
+                """
+                input[0] = [[ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists:true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists:true)
+                    ],
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fasta - sarscov2 - stub") {
+        options '-stub'
+
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [[ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fastq - sarscov2 - stub") {
+        options '-stub'
+
+        when {
+            params {
+                module_args = '-r'
+            }
+            process {
+                """
+                input[0] = [[ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists:true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists:true)
+                    ],
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/stecfinder/tests/main.nf.test.snap b/modules/nf-core/stecfinder/tests/main.nf.test.snap
new file mode 100644
index 000000000000..c902675e15ac
--- /dev/null
+++ b/modules/nf-core/stecfinder/tests/main.nf.test.snap
@@ -0,0 +1,134 @@
+{
+    "fastq - sarscov2 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:14:28.714589218"
+    },
+    "fasta - sarscov2": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,c17e1e69728b48c06c47a7d10086f1da"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,c17e1e69728b48c06c47a7d10086f1da"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:13:58.436995675"
+    },
+    "fasta - sarscov2 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:14:18.667066355"
+    },
+    "fastq - sarscov2": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,f0a5c4e3509bc8bd03f09aa21c31c526"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,f0a5c4e3509bc8bd03f09aa21c31c526"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2c48214785500e9b7a54d6ce8949a1c1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T13:14:08.559641764"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/stecfinder/tests/nextflow.config b/modules/nf-core/stecfinder/tests/nextflow.config
new file mode 100644
index 000000000000..f42621e171f1
--- /dev/null
+++ b/modules/nf-core/stecfinder/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "STECFINDER" {
+        ext.args = params.module_args
+    }
+}
diff --git a/modules/nf-core/survivor/filter/tests/main.nf.test b/modules/nf-core/survivor/filter/tests/main.nf.test
new file mode 100644
index 000000000000..da590bd07e66
--- /dev/null
+++ b/modules/nf-core/survivor/filter/tests/main.nf.test
@@ -0,0 +1,93 @@
+nextflow_process {
+
+    name "Test Process SURVIVOR_FILTER"
+    script "../main.nf"
+    process "SURVIVOR_FILTER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "survivor"
+    tag "survivor/filter"
+
+    test("homo sapiens - vcf") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    []
+                    ]
+                input[1] = 51
+                input[2] = 10001
+                input[3] = 0.01
+                input[4] = 10
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf - bed") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                    ]
+                input[1] = 51
+                input[2] = 10001
+                input[3] = 0.01
+                input[4] = 10
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    []
+                    ]
+                input[1] = 51
+                input[2] = 10001
+                input[3] = 0.01
+                input[4] = 10
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/survivor/filter/tests/main.nf.test.snap b/modules/nf-core/survivor/filter/tests/main.nf.test.snap
new file mode 100644
index 000000000000..413707aaaca6
--- /dev/null
+++ b/modules/nf-core/survivor/filter/tests/main.nf.test.snap
@@ -0,0 +1,101 @@
+{
+    "homo sapiens - vcf - bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,ec23f83ba5bb098d45027e63fab93d05"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a18e3b02957801e91625dbe16cf80034"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,ec23f83ba5bb098d45027e63fab93d05"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a18e3b02957801e91625dbe16cf80034"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-07T17:52:18.534971"
+    },
+    "homo sapiens - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,ec23f83ba5bb098d45027e63fab93d05"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a18e3b02957801e91625dbe16cf80034"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,ec23f83ba5bb098d45027e63fab93d05"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a18e3b02957801e91625dbe16cf80034"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-07T17:52:13.987478"
+    },
+    "homo sapiens - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a18e3b02957801e91625dbe16cf80034"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a18e3b02957801e91625dbe16cf80034"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T11:51:42.268146"
+    }
+}
diff --git a/modules/nf-core/survivor/simsv/tests/main.nf.test b/modules/nf-core/survivor/simsv/tests/main.nf.test
new file mode 100644
index 000000000000..ef8b0f5d2923
--- /dev/null
+++ b/modules/nf-core/survivor/simsv/tests/main.nf.test
@@ -0,0 +1,122 @@
+nextflow_process {
+
+    name "Test Process SURVIVOR_SIMSV"
+    script "../main.nf"
+    process "SURVIVOR_SIMSV"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "survivor"
+    tag "survivor/simsv"
+
+    test("homo sapiens - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                [ id:'fasta'], // meta map
+                file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
+                input[1] = [
+                [ id:'fai'], // meta map
+                file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
+                input[2] = [[], []]
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+    test("homo sapiens - fasta - parameters") {
+        when {
+            process {
+                """
+            // generate parameter file
+            parameters = Channel.of(
+'''PARAMETER FILE: DO JUST MODIFY THE VALUES AND KEEP THE SPACES!
+DUPLICATION_minimum_length: 100
+DUPLICATION_maximum_length: 10000
+DUPLICATION_number: 3
+INDEL_minimum_length: 20
+INDEL_maximum_length: 500
+INDEL_number: 1
+TRANSLOCATION_minimum_length: 1000
+TRANSLOCATION_maximum_length: 3000
+TRANSLOCATION_number: 0
+INVERSION_minimum_length: 600
+INVERSION_maximum_length: 800
+INVERSION_number: 4
+INV_del_minimum_length: 600
+INV_del_maximum_length: 800
+INV_del_number: 2
+INV_dup_minimum_length: 600
+INV_dup_maximum_length: 800
+INV_dup_number: 2'''
+                ).collectFile(name:"parameters.txt", newLine:true)
+                .map { [[id:"parameters"], it] }
+
+                input[0] = [
+                [ id:'fasta'], // meta map
+                file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
+                input[1] = [
+                [ id:'fai'], // meta map
+                file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
+                input[2] = parameters
+                input[3] = 1
+                input[4] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.vcf[0][1]).name, // unstable
+                    file(process.out.insertions[0][1]).name, // unstable
+                    file(process.out.fasta[0][1]).name, // unstable
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+    test("homo sapiens - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                [ id:'fasta'], // meta map
+                file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
+                input[1] = [
+                [ id:'fai'], // meta map
+                file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
+                input[2] = [[], []]
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/survivor/simsv/tests/main.nf.test.snap b/modules/nf-core/survivor/simsv/tests/main.nf.test.snap
new file mode 100644
index 000000000000..a3d9b27e1fa5
--- /dev/null
+++ b/modules/nf-core/survivor/simsv/tests/main.nf.test.snap
@@ -0,0 +1,141 @@
+{
+    "homo sapiens - fasta - parameters": {
+        "content": [
+            "fasta.vcf",
+            "fasta.insertions.fa",
+            "fasta.fasta",
+            [
+                "versions.yml:md5,899f0b900c2bb07d24e74b76a4160af6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T17:27:15.40472"
+    },
+    "homo sapiens - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "fasta"
+                        },
+                        "fasta.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "fasta"
+                        },
+                        "fasta.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    "versions.yml:md5,899f0b900c2bb07d24e74b76a4160af6"
+                ],
+                "bed": [
+                    
+                ],
+                "fasta": [
+                    
+                ],
+                "insertions": [
+                    
+                ],
+                "parameters": [
+                    [
+                        {
+                            "id": "fasta"
+                        },
+                        "fasta.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "fasta"
+                        },
+                        "fasta.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,899f0b900c2bb07d24e74b76a4160af6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-08T17:23:24.09006"
+    },
+    "homo sapiens - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "fasta"
+                        },
+                        "fasta.txt:md5,a95bd884130aebbb9fde02184bc7ca81"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    "versions.yml:md5,899f0b900c2bb07d24e74b76a4160af6"
+                ],
+                "bed": [
+                    
+                ],
+                "fasta": [
+                    
+                ],
+                "insertions": [
+                    
+                ],
+                "parameters": [
+                    [
+                        {
+                            "id": "fasta"
+                        },
+                        "fasta.txt:md5,a95bd884130aebbb9fde02184bc7ca81"
+                    ]
+                ],
+                "vcf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,899f0b900c2bb07d24e74b76a4160af6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-07T20:06:47.203984"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/svtk/rdtest2vcf/main.nf b/modules/nf-core/svtk/rdtest2vcf/main.nf
index 796650af527e..203551724d99 100644
--- a/modules/nf-core/svtk/rdtest2vcf/main.nf
+++ b/modules/nf-core/svtk/rdtest2vcf/main.nf
@@ -31,6 +31,18 @@ process SVTK_RDTEST2VCF {
         ${prefix}.vcf.gz \\
         ${contigs}
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svtk: ${VERSION}
+    END_VERSIONS
+    """
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.0.20190615' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    echo "" | gzip > ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         svtk: ${VERSION}
diff --git a/modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test b/modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test
new file mode 100644
index 000000000000..967c7bba37c1
--- /dev/null
+++ b/modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test
@@ -0,0 +1,94 @@
+nextflow_process {
+
+    name "Test Process SVTK_RDTEST2VCF"
+    script "../main.nf"
+    process "SVTK_RDTEST2VCF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "svtk"
+    tag "svtk/rdtest2vcf"
+    tag "svtk/vcf2bed"
+    tag "manta/germline"
+
+    test("homo sapiens - vcf") {
+
+        setup {
+            run("MANTA_GERMLINE") {
+                script "modules/nf-core/manta/germline/main.nf"
+                process {
+                    """
+                    input[0] = [ [ id:'test'], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                                [],[]
+                            ]
+                    input[1] = [ [id:'genome'],
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                            ]
+                    input[2] = [ [id:'genome'],
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                            ]
+                    input[3] = Channel.of("[manta]", "enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 0")
+                                .collectFile(name:"manta_options.ini", newLine:true)
+                    """
+                }
+            }
+            run("SVTK_VCF2BED") {
+                script "modules/nf-core/svtk/vcf2bed/main.nf"
+                process {
+                    """
+                    input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by:0)
+
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                // generate samples file
+                samples  = Channel.of("test").collectFile(name: "samples.txt")
+                input[0] = SVTK_VCF2BED.out.bed.combine(samples)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - bed - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // generate samples file
+                samples  = Channel.of("test").collectFile(name: "samples.txt")
+                input[0] = Channel.from(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                                    .map{it -> [["test"], it]}.collect().combine(samples, by: 0)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test.snap b/modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test.snap
new file mode 100644
index 000000000000..fc5cb0325542
--- /dev/null
+++ b/modules/nf-core/svtk/rdtest2vcf/tests/main.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "homo sapiens - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,17b6ce06b0b0a8a82de0b6cc7d0f51a1"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,907b056296ef8f6c060b73fb8659d8e6"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,17b6ce06b0b0a8a82de0b6cc7d0f51a1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,907b056296ef8f6c060b73fb8659d8e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-09T12:36:07.200622"
+    },
+    "homo sapiens - bed - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-09T12:42:03.933697"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/svtk/standardize/environment.yml b/modules/nf-core/svtk/standardize/environment.yml
index d349bc0ac9a7..5883bdb459f0 100644
--- a/modules/nf-core/svtk/standardize/environment.yml
+++ b/modules/nf-core/svtk/standardize/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::svtk=0.0.20190615
+  - bioconda::svtk=0.0.20190615=*2
diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf
index 52e8eb7d3da5..7eb71b5661ce 100644
--- a/modules/nf-core/svtk/standardize/main.nf
+++ b/modules/nf-core/svtk/standardize/main.nf
@@ -8,12 +8,12 @@ process SVTK_STANDARDIZE {
         'biocontainers/svtk:0.0.20190615--py37h73a75cf_2' }"
 
     input:
-    tuple val(meta), path(vcf)
-    path fasta_fai
+    tuple val(meta), path(input)
+    tuple val(meta2), path (fai)
 
     output:
-    tuple val(meta), path("*.std.vcf.gz"), emit: standardized_vcf
-    path "versions.yml"                  , emit: versions
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,21 +21,32 @@ process SVTK_STANDARDIZE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
-    def arguments   = args.args     ?: ''
-    def caller      = args.caller   ?: 'delly'
-
+    def contigs = fai ? "--contigs ${fai}" : ""
     def VERSION = '0.0.20190615' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
-    def contigs = fasta_fai ? "--contigs ${fasta_fai}" : ""
+    if ("$input" == "${prefix}.vcf.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     """
     svtk standardize \\
-        ${arguments} \\
+        $args \\
         ${contigs} \\
-        ${vcf} \\
-        ${prefix}.std.vcf.gz \\
-        ${caller}
+        ${input} \\
+        ${prefix}.vcf.gz \\
+        $meta.caller
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svtk: ${VERSION}
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.0.20190615' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    if ("$input" == "${prefix}.vcf.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    echo | gzip > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/svtk/standardize/meta.yml b/modules/nf-core/svtk/standardize/meta.yml
index 84090cbacdd6..b1a0b521e73b 100644
--- a/modules/nf-core/svtk/standardize/meta.yml
+++ b/modules/nf-core/svtk/standardize/meta.yml
@@ -19,28 +19,32 @@ input:
   - - meta:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - vcf:
+          Groovy Map containing sample information. Caller can be one of the tools: delly, manta, melt, wham
+          e.g. [ id:'test', caller:"delly" ]
+    - input:
         type: file
         description: A gzipped VCF file to be standardized
         pattern: "*.vcf.gz"
-  - - fasta_fai:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test2' ]
+    - fai:
         type: file
-        description: Optional fasta index file that specifies the contigs to be used
-          in the VCF header (defaults to all contigs of GRCh37)
+        description: Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)
         pattern: "*.fai"
 output:
-  - standardized_vcf:
+  - vcf:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.std.vcf.gz":
+            e.g. [ id:'test', caller:"delly" ]
+      - "*.vcf.gz":
           type: file
           description: A gzipped version of the standardized VCF file
-          pattern: "*.std.vcf.gz"
+          pattern: "*.vcf.gz"
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/svtk/standardize/tests/main.nf.test b/modules/nf-core/svtk/standardize/tests/main.nf.test
new file mode 100644
index 000000000000..3dca53f9bb7a
--- /dev/null
+++ b/modules/nf-core/svtk/standardize/tests/main.nf.test
@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process SVTK_STANDARDIZE"
+    script "../main.nf"
+    process "SVTK_STANDARDIZE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "svtk"
+    tag "svtk/standardize"
+
+    test("homo sapiens - vcf.gz") {
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', caller:'manta'], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz', checkIfExists: true)
+				]
+                input[1] = [
+                    [id:'fai'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', caller:'manta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz', checkIfExists: true)
+				]
+                input[1] = [
+                    [id:'fai'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/svtk/standardize/tests/main.nf.test.snap b/modules/nf-core/svtk/standardize/tests/main.nf.test.snap
new file mode 100644
index 000000000000..d4ec0ad7b04f
--- /dev/null
+++ b/modules/nf-core/svtk/standardize/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "homo sapiens - vcf.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "caller": "manta"
+                        },
+                        "test.vcf.gz:md5,6119075b757b3720ab5ecb484c4c8b70"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e2e8ab223b67146188badb065515d8dc"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "caller": "manta"
+                        },
+                        "test.vcf.gz:md5,6119075b757b3720ab5ecb484c4c8b70"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e2e8ab223b67146188badb065515d8dc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-11T11:52:24.533119"
+    },
+    "homo sapiens - vcf.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "caller": "manta"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e2e8ab223b67146188badb065515d8dc"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "caller": "manta"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e2e8ab223b67146188badb065515d8dc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-11T11:52:29.264333"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sylphtax/merge/environment.yml b/modules/nf-core/sylphtax/merge/environment.yml
new file mode 100644
index 000000000000..517edcad5ef3
--- /dev/null
+++ b/modules/nf-core/sylphtax/merge/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::sylph-tax=1.2.0"
diff --git a/modules/nf-core/sylphtax/merge/main.nf b/modules/nf-core/sylphtax/merge/main.nf
new file mode 100644
index 000000000000..7d0ab8fde8c1
--- /dev/null
+++ b/modules/nf-core/sylphtax/merge/main.nf
@@ -0,0 +1,51 @@
+
+process SYLPHTAX_MERGE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sylph-tax:1.2.0--pyhdfd78af_0':
+        'biocontainers/sylph-tax:1.2.0--pyhdfd78af_0' }"
+
+
+    input:
+    tuple val(meta), path(sylphtax_reports)
+    val data_type
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
+    sylph-tax \\
+        merge \\
+        ${sylphtax_reports} \\
+        --column $data_type \\
+        --output ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sylph-tax: \$(sylph-tax --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sylph-tax: \$(sylph-tax --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/sylphtax/merge/meta.yml b/modules/nf-core/sylphtax/merge/meta.yml
new file mode 100644
index 000000000000..1cce3bb14172
--- /dev/null
+++ b/modules/nf-core/sylphtax/merge/meta.yml
@@ -0,0 +1,46 @@
+name: "sylphtax_merge"
+description: Merge multiple taxonomic profiles from sylphtaxt/taxprof into a tsv table
+keywords:
+  - sylph
+  - metagenomics
+  - merge
+tools:
+  - sylphtax:
+      description: Integrating taxonomic information into the sylph metagenome profiler.
+      homepage: https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file
+      documentation: https://sylph-docs.github.io/sylph-tax/
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - sylphtax_reports:
+        type: file
+        description: Output taxonomic profile from sylph-tax taxprof command.
+        pattern: "*.{sylphmpa}"
+  - - data_type:
+        type: string
+        description: Can be ANI, relative abundance, or sequence abundance.
+output:
+  - tsv:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tsv":
+          type: file
+          description: Output profile with the merged taxonomic profiles in tsv format.
+          pattern: "*.tsv"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@sofstam"
+maintainers:
+  - "@sofstam"
diff --git a/modules/nf-core/sylphtax/merge/tests/main.nf.test b/modules/nf-core/sylphtax/merge/tests/main.nf.test
new file mode 100644
index 000000000000..19879eff6f20
--- /dev/null
+++ b/modules/nf-core/sylphtax/merge/tests/main.nf.test
@@ -0,0 +1,116 @@
+nextflow_process {
+
+    name "Test Process SYLPHTAX_MERGE"
+    script "../main.nf"
+    process "SYLPHTAX_MERGE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sylph"
+    tag "sylph/profile"
+    tag "sylphtax"
+    tag "sylphtax/taxprof"
+    tag "sylphtax/merge"
+
+
+    test("sarscov2 illumina single-end [fastq_gz]") {
+        setup {
+            run("SYLPH_PROFILE") {
+                script "../../../sylph/profile/main.nf"
+                process {
+                """
+                input[0] = [
+                            [ id:'test', single_end:false ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ]
+                input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+                }
+            }
+            run("SYLPHTAX_TAXPROF")
+            {
+                script "../../../sylphtax/taxprof/main.nf"
+                process {
+                """
+                input[0] = SYLPH_PROFILE.out.profile_out
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true)
+                """
+                }
+            }
+
+        }
+        when {
+
+            process {
+                """
+                input[0] = SYLPHTAX_TAXPROF.out.taxprof_output
+                input[1] = "relative_abundance"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.tsv
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 illumina single-end [fastq_gz]-stub") {
+
+        options '-stub'
+
+        setup {
+            run("SYLPH_PROFILE") {
+                script "../../../sylph/profile/main.nf"
+                process {
+                """
+                input[0] = [
+                            [ id:'test', single_end:false ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ]
+                input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+                }
+            }
+            run("SYLPHTAX_TAXPROF")
+            {
+                script "../../../sylphtax/taxprof/main.nf"
+                process {
+                """
+                input[0] = SYLPH_PROFILE.out.profile_out
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true)
+                """
+                }
+            }
+
+        }
+        when {
+
+            process {
+                """
+                input[0] = SYLPHTAX_TAXPROF.out.taxprof_output
+                input[1] = "relative_abundance"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.tsv
+                ).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/sylphtax/merge/tests/main.nf.test.snap b/modules/nf-core/sylphtax/merge/tests/main.nf.test.snap
new file mode 100644
index 000000000000..73c89e5a8f09
--- /dev/null
+++ b/modules/nf-core/sylphtax/merge/tests/main.nf.test.snap
@@ -0,0 +1,44 @@
+{
+    "sarscov2 illumina single-end [fastq_gz]": {
+        "content": [
+            [
+                "versions.yml:md5,fb665700c08de369d03e29c02394da07"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.tsv:md5,0babfd085a52f127c5d352fab5595b39"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-07T15:29:34.708536546"
+    },
+    "sarscov2 illumina single-end [fastq_gz]-stub": {
+        "content": [
+            [
+                "versions.yml:md5,fb665700c08de369d03e29c02394da07"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-07T15:29:46.390759044"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sylphtax/taxprof/environment.yml b/modules/nf-core/sylphtax/taxprof/environment.yml
index f35891d9ae06..517edcad5ef3 100644
--- a/modules/nf-core/sylphtax/taxprof/environment.yml
+++ b/modules/nf-core/sylphtax/taxprof/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::sylph-tax=1.1.2"
+  - "bioconda::sylph-tax=1.2.0"
diff --git a/modules/nf-core/sylphtax/taxprof/main.nf b/modules/nf-core/sylphtax/taxprof/main.nf
index 3f71775586be..d7508b3a5a51 100644
--- a/modules/nf-core/sylphtax/taxprof/main.nf
+++ b/modules/nf-core/sylphtax/taxprof/main.nf
@@ -5,8 +5,8 @@ process SYLPHTAX_TAXPROF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sylph-tax:1.1.2--pyhdfd78af_0':
-        'biocontainers/sylph-tax:1.1.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sylph-tax:1.2.0--pyhdfd78af_0':
+        'biocontainers/sylph-tax:1.2.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(sylph_results)
@@ -24,6 +24,7 @@ process SYLPHTAX_TAXPROF {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
+    export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
     sylph-tax \\
         taxprof \\
         $sylph_results \\
@@ -31,21 +32,22 @@ process SYLPHTAX_TAXPROF {
         -t $taxonomy
 
     mv *.sylphmpa ${prefix}.sylphmpa
-    
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1)
+        sylph-tax: \$(sylph-tax --version)
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
     touch ${prefix}.sylphmpa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1)
+        sylph-tax: \$(sylph-tax --version)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/sylphtax/taxprof/meta.yml b/modules/nf-core/sylphtax/taxprof/meta.yml
index e4ee39ba0dbf..02d7780d3b72 100644
--- a/modules/nf-core/sylphtax/taxprof/meta.yml
+++ b/modules/nf-core/sylphtax/taxprof/meta.yml
@@ -1,51 +1,51 @@
 name: sylphtax_taxprof
 description: Incorporates taxonomy into sylph metagenomic classifier
 keywords:
-- taxonomy
-- sylph
-- metagenomics
+  - taxonomy
+  - sylph
+  - metagenomics
 tools:
-- sylphtax:
-    description: Integrating taxonomic information into the sylph metagenome profiler.
-    homepage: https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file
-    documentation: https://sylph-docs.github.io/sylph-tax/
-    licence: ["MIT"]
-    identifier: ''
+  - sylphtax:
+      description: Integrating taxonomic information into the sylph metagenome profiler.
+      homepage: https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file
+      documentation: https://sylph-docs.github.io/sylph-tax/
+      licence: ["MIT"]
+      identifier: ""
 input:
-- - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  - sylph_results:
-      type: file
-      description: Output results from sylph classifier. The database file(s) used to create this file with sylph must be the same as those of the taxonomy input channel of this module.
-      pattern: "*.{tsv}"
-- - taxonomy:
-      type: file
-      description: A list of sylph-tax identifiers (e.g. GTDB_r220 or IMGVR_4.1).
-        Multiple taxonomy metadata files can be input. Custom taxonomy files are also
-        possible.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - sylph_results:
+        type: file
+        description: Output results from sylph classifier. The database file(s) used to create this file with sylph must be the same as those of the taxonomy input channel of this module.
+        pattern: "*.{tsv}"
+  - - taxonomy:
+        type: file
+        description: A list of sylph-tax identifiers (e.g. GTDB_r220 or IMGVR_4.1).
+          Multiple taxonomy metadata files can be input. Custom taxonomy files are also
+          possible.
 output:
-- taxprof_output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-      pattern: "*{.sylphmpa}"
-  - '*.sylphmpa':
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-      pattern: "*{.sylphmpa}"
-- versions:
-  - versions.yml:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  - taxprof_output:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*{.sylphmpa}"
+      - "*.sylphmpa":
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*{.sylphmpa}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
-- "@sofstam"
+  - "@sofstam"
 maintainers:
-- "@sofstam"
+  - "@sofstam"
diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap
index 824ceb3edbba..3c26e75ec9a8 100644
--- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap
+++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "stub sarscov2 illumina single-end [fastq_gz]": {
         "content": [
             [
-                "versions.yml:md5,976fae8d146f4f3087e2a090703f09b9"
+                "versions.yml:md5,bdbbd22b3e721ba2027d3e6cb1dc4bb4"
             ],
             [
                 [
@@ -17,12 +17,12 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-06T09:50:24.907781877"
+        "timestamp": "2025-04-07T15:28:04.026470884"
     },
     "sarscov2 illumina single-end [fastq_gz]": {
         "content": [
             [
-                "versions.yml:md5,976fae8d146f4f3087e2a090703f09b9"
+                "versions.yml:md5,bdbbd22b3e721ba2027d3e6cb1dc4bb4"
             ],
             [
                 [
@@ -30,7 +30,7 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test.sylphmpa:md5,797e3463eeb9a2e8f91de9b842cd421d"
+                    "test.sylphmpa:md5,a9743c21a53ba766226e57d2a25f6167"
                 ]
             ]
         ],
@@ -38,6 +38,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-06T09:50:17.295239617"
+        "timestamp": "2025-04-07T15:27:55.45776116"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ultra/index/tests/main.nf.test b/modules/nf-core/ultra/index/tests/main.nf.test
deleted file mode 100644
index 3e3e82bbce8d..000000000000
--- a/modules/nf-core/ultra/index/tests/main.nf.test
+++ /dev/null
@@ -1,51 +0,0 @@
-nextflow_process {
-
-    name "Test Process ULTRA_INDEX"
-    config "./nextflow.config"
-    script "../main.nf"
-    process "ULTRA_INDEX"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "ultra"
-    tag "ultra/index"
-    tag "gnu"
-    tag "gnu/sort"
-
-    test("test_ultra_index") {
-
-        setup {
-            run("GNU_SORT") {
-                script "../../../gnu/sort/main.nf"
-
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf',checkIfExists:true)
-                        ]
-                    """
-                }
-            }
-        }
-
-        when {
-            params {
-                sort_args   = '-k1,1 -k4,4n'
-                module_args = '--disable_infer'
-            }
-            process {
-                """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta',checkIfExists:true)
-                input[1] = GNU_SORT.out.sorted.map{it[1]}
-                """
-            }
-        }
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/ultra/index/tests/main.nf.test.snap b/modules/nf-core/ultra/index/tests/main.nf.test.snap
deleted file mode 100644
index 0165f8469c4b..000000000000
--- a/modules/nf-core/ultra/index/tests/main.nf.test.snap
+++ /dev/null
@@ -1,73 +0,0 @@
-{
-    "test_ultra_index": {
-        "content": [
-            {
-                "0": [
-                    [
-                        [
-                            "all_splice_pairs_annotations.pickle:md5,ec60c02903edc30a3f10c196c425fb16",
-                            "all_splice_sites_annotations.pickle:md5,5a7d640f4e707acb37966542c132455a",
-                            "chr_to_id.pickle:md5,b8aa0a986ec685f5f7e8fad651ff1b90",
-                            "exon_choordinates_to_id.pickle:md5,4e978d727a90e2b225c5ff4bc6107578",
-                            "flank_choordinates.pickle:md5,309e3de05b9d781e01810ea442ebf2ef",
-                            "gene_to_small_segments.pickle:md5,37a25f3ba84edac017ecb9e946081696",
-                            "id_to_chr.pickle:md5,020263c6d9f399670871ca187c1d203f",
-                            "max_intron_chr.pickle:md5,f568beb2f859d8e9b1f2993048e4fcd2",
-                            "parts_to_segments.pickle:md5,56950e119f074e4b4577dc3cbf00ea76",
-                            "ref_exon_sequences.pickle:md5,860192c5711d1b41bda2d3677cf310f5",
-                            "ref_flank_sequences.pickle:md5,9b81749e32c4e4f742590218e8854313",
-                            "ref_part_sequences.pickle:md5,3354b0d8f8f1c9db1a98d70e470826ff",
-                            "ref_segment_sequences.pickle:md5,fe89d6588433b848a2055395765032a6",
-                            "refs_id_lengths.pickle:md5,102873a7c330dc1ca562a699dec2d5f2",
-                            "refs_lengths.pickle:md5,93012591af522a2f6a6c1620f23aa065",
-                            "segment_id_to_choordinates.pickle:md5,59689a3f3e8bebb1938d576932f266f8",
-                            "segment_to_gene.pickle:md5,b27dbc0e09354a637c453a9130aae260",
-                            "segment_to_ref.pickle:md5,628eb8bd24cda6f7dd6a2de7f591ffda",
-                            "splices_to_transcripts.pickle:md5,4b7d114268be85793fa0b2de64c8adbe",
-                            "transcripts_to_splices.pickle:md5,3e307206909ed029a69b65f6afca02d0"
-                        ],
-                        "database.db:md5,f9b780bf5a0a5d23256afb99df7137d9"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,45fdc5637701f0c91e005244cc09a199"
-                ],
-                "index": [
-                    [
-                        [
-                            "all_splice_pairs_annotations.pickle:md5,ec60c02903edc30a3f10c196c425fb16",
-                            "all_splice_sites_annotations.pickle:md5,5a7d640f4e707acb37966542c132455a",
-                            "chr_to_id.pickle:md5,b8aa0a986ec685f5f7e8fad651ff1b90",
-                            "exon_choordinates_to_id.pickle:md5,4e978d727a90e2b225c5ff4bc6107578",
-                            "flank_choordinates.pickle:md5,309e3de05b9d781e01810ea442ebf2ef",
-                            "gene_to_small_segments.pickle:md5,37a25f3ba84edac017ecb9e946081696",
-                            "id_to_chr.pickle:md5,020263c6d9f399670871ca187c1d203f",
-                            "max_intron_chr.pickle:md5,f568beb2f859d8e9b1f2993048e4fcd2",
-                            "parts_to_segments.pickle:md5,56950e119f074e4b4577dc3cbf00ea76",
-                            "ref_exon_sequences.pickle:md5,860192c5711d1b41bda2d3677cf310f5",
-                            "ref_flank_sequences.pickle:md5,9b81749e32c4e4f742590218e8854313",
-                            "ref_part_sequences.pickle:md5,3354b0d8f8f1c9db1a98d70e470826ff",
-                            "ref_segment_sequences.pickle:md5,fe89d6588433b848a2055395765032a6",
-                            "refs_id_lengths.pickle:md5,102873a7c330dc1ca562a699dec2d5f2",
-                            "refs_lengths.pickle:md5,93012591af522a2f6a6c1620f23aa065",
-                            "segment_id_to_choordinates.pickle:md5,59689a3f3e8bebb1938d576932f266f8",
-                            "segment_to_gene.pickle:md5,b27dbc0e09354a637c453a9130aae260",
-                            "segment_to_ref.pickle:md5,628eb8bd24cda6f7dd6a2de7f591ffda",
-                            "splices_to_transcripts.pickle:md5,4b7d114268be85793fa0b2de64c8adbe",
-                            "transcripts_to_splices.pickle:md5,3e307206909ed029a69b65f6afca02d0"
-                        ],
-                        "database.db:md5,f9b780bf5a0a5d23256afb99df7137d9"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,45fdc5637701f0c91e005244cc09a199"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-04-01T13:48:22.364563262"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/ultra/index/tests/nextflow.config b/modules/nf-core/ultra/index/tests/nextflow.config
deleted file mode 100644
index 5d52e18c0d31..000000000000
--- a/modules/nf-core/ultra/index/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-    withName: "GNU_SORT" {
-        ext.args = params.sort_args
-    }
-
-    withName: "ULTRA_INDEX" {
-        ext.args = params.module_args
-    }
-}
diff --git a/modules/nf-core/variancepartition/dream/main.nf b/modules/nf-core/variancepartition/dream/main.nf
index c9fa12dabfbe..c3b4a59ff0fd 100644
--- a/modules/nf-core/variancepartition/dream/main.nf
+++ b/modules/nf-core/variancepartition/dream/main.nf
@@ -1,5 +1,5 @@
 process VARIANCEPARTITION_DREAM {
-    tag "${meta.id} - ${meta.contrast_id}"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
@@ -8,10 +8,12 @@ process VARIANCEPARTITION_DREAM {
         'community.wave.seqera.io/library/bioconductor-edger_bioconductor-variancepartition_r-optparse:ba778938d72f30c5' }"
 
     input:
-    tuple val(meta), path(samplesheet), path(counts)
+    tuple val(meta), val(contrast_variable), val(reference), val(target), val(formula)
+    tuple val(meta2), path(samplesheet), path(counts)
 
     output:
     tuple val(meta), path("*.dream.results.tsv")        , emit: results
+    tuple val(meta), path("*.dream.model.txt")          , emit: model
     path "versions.yml"                                 , emit: versions
 
     when:
@@ -21,9 +23,9 @@ process VARIANCEPARTITION_DREAM {
     template 'dream.R'
 
     stub:
-    prefix = task.ext.prefix   ?: "${meta.id}"
     """
-    touch "${meta.contrast_id}.dream.results.tsv"
+    touch "${meta.id}.dream.results.tsv"
+    touch "${meta.id}.dream.model.txt"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/variancepartition/dream/meta.yml b/modules/nf-core/variancepartition/dream/meta.yml
index da5b3a900d4d..48011b8451b7 100644
--- a/modules/nf-core/variancepartition/dream/meta.yml
+++ b/modules/nf-core/variancepartition/dream/meta.yml
@@ -18,16 +18,30 @@ input:
   - - meta:
         type: map
         description: |
-          Groovy Map containing run and contrast information. This can be used at the
-          workflow level to pass optional parameters to the module, e.g.
-          [
-            contrast_id: 'treatment_mCherry_hND6',
-            contrast_variable: 'treatment',
-            contrast_reference: 'mCherry',
-            contrast_target: 'hND6',
-            formula: '~ treatment + (1 | sample_number)'
-          ]
-          Plus mandatory `id` and other fields created along the run.
+          Groovy Map containing run and contrast information.
+    - contrast_variable:
+        type: string
+        description: |
+          The column in the sample sheet that should be used to define groups for
+          comparison
+    - reference:
+        type: string
+        description: |
+          The value within the contrast_variable column of the sample sheet that
+          should be used to derive the reference samples
+    - target:
+        type: string
+        description: |
+          The value within the contrast_variable column of the sample sheet that
+          should be used to derive the target samples
+    - formula:
+        type: string
+        description: (Mandatory) R formula string used for modeling, e.g. '~ treatment + (1 | sample_number)'.
+  - - meta2:
+        type: map
+        description: |
+          Groovy map containing study-wide metadata related to the sample sheet
+          and matrix
     - samplesheet:
         type: file
         description: Sample sheet file containing sample metadata.
@@ -35,8 +49,7 @@ input:
     - counts:
         type: file
         description: |
-          Raw TSV or CSV format expression matrix with count data by row and samples
-          by column
+          TSV or CSV format expression matrix with genes as rows and samples as columns.
         ontologies: []
 output:
   - results:
@@ -49,13 +62,25 @@ output:
           description: |
             TSV-format table of differential expression information as output by Dream
           pattern: "*.dream.results.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  - model:
+      - meta:
+          type: map
+          description: Metadata map passed through from input.
+      - "*.dream.model.txt":
+          type: file
+          description: |
+            R model description text file.
+          pattern: "*.dream.model.txt"
           ontologies: []
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
-          ontologies: []
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@alanmmobbs03"
   - "@nschcolnicov"
diff --git a/modules/nf-core/variancepartition/dream/templates/dream.R b/modules/nf-core/variancepartition/dream/templates/dream.R
index 653fd459004a..3bd8c627989a 100644
--- a/modules/nf-core/variancepartition/dream/templates/dream.R
+++ b/modules/nf-core/variancepartition/dream/templates/dream.R
@@ -47,12 +47,12 @@ read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.nam
 
 # Options list
 opt <- list(
-    output_prefix      = "$meta.contrast_id",       # Prefix for output files
+    output_prefix      = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'),
     count_file         = "$counts",                 # File containing raw counts
     sample_file        = "$samplesheet",            # File containing sample information
-    contrast_variable  = "$meta.contrast_variable", # Variable for contrast (e.g., "treatment")
-    contrast_reference    = "$meta.contrast_reference",# Reference level for the contrast
-    contrast_target       = "$meta.contrast_target",   # Target level for the contrast (e.g., "mCherry")
+    contrast_variable  = "$contrast_variable",      # Variable for contrast (e.g., "treatment")
+    contrast_reference = "$reference",              # Reference level for the contrast
+    contrast_target    = "$target",                 # Target level for the contrast (e.g., "mCherry")
     sample_id_col      = "sample",                  # Column name for sample IDs
     threads            = "$task.cpus",              # Number of threads for multithreading
     subset_to_contrast_samples = FALSE,            # Whether to subset to contrast samples
@@ -69,7 +69,7 @@ opt <- list(
     winsor_tail_p      = "0.05,0.1",              # Winsor tail probabilities for eBayes
     ddf                = "adaptive",              # 'Satterthwaite', 'Kenward-Roger', or 'adaptive'
     reml               = FALSE,
-    formula            = "$meta.formula",         # User-specified formula (e.g. "~ + (1 | sample_number)")
+    formula            = "$formula",              # User-specified formula (e.g. "~ + (1 | sample_number)")
     apply_voom         = FALSE                    # Whether to apply `voomWithDreamWeights`
 )
 
@@ -159,6 +159,9 @@ results <- topTable(fitmm, coef = coef_name,
 write.table(results, file = paste(opt\$output_prefix, 'dream.results.tsv', sep = '.'),
             col.names = TRUE, row.names = FALSE, sep = '\t', quote = FALSE )
 
+# Save model to file
+write(deparse(form), file=paste(opt\$output_prefix, 'dream.model.txt', sep = '.'))
+
 ################################################
 ################################################
 ## VERSIONS FILE                              ##
diff --git a/modules/nf-core/variancepartition/dream/tests/main.nf.test b/modules/nf-core/variancepartition/dream/tests/main.nf.test
index 107e238f16fd..319e444dcaa9 100644
--- a/modules/nf-core/variancepartition/dream/tests/main.nf.test
+++ b/modules/nf-core/variancepartition/dream/tests/main.nf.test
@@ -14,17 +14,13 @@ nextflow_process {
         when {
             process {
                 """
-                // contrast data + counts + samplesheet
-                input[0] = Channel.of(
-                    [
-                        [
-                            contrast_id: 'treatment_mCherry_hND6',
-                            contrast_variable: 'treatment',
-                            contrast_reference: 'mCherry',
-                            contrast_target: 'hND6',
-                            blocking_factors: null,
-                            formula: null
-                        ],
+                input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':null, 'formula':null])
+                    .map{
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
+                    }
+
+                input[1] = Channel.of([
+                    [ id:'test' ],
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv", checkIfExists: true),
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv", checkIfExists: true)
                     ]
@@ -45,17 +41,13 @@ nextflow_process {
         when {
             process {
                 """
-                // contrast data + counts + samplesheet
-                input[0] = Channel.of(
-                    [
-                        [
-                            contrast_id: 'treatment_mCherry_hND6',
-                            contrast_variable: 'treatment',
-                            contrast_reference: 'mCherry',
-                            contrast_target: 'hND6',
-                            blocking_factors: 'sample_number',
-                            formula: '~ treatment + (1 | sample_number)'
-                        ],
+                input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ treatment + (1 | sample_number)'])
+                    .map{
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
+                    }
+
+                input[1] = Channel.of([
+                    [ id:'test' ],
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv", checkIfExists: true),
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv", checkIfExists: true)
                     ]
@@ -78,17 +70,13 @@ nextflow_process {
         when {
             process {
                 """
-                // contrast data + counts + samplesheet
-                input[0] = Channel.of(
-                    [
-                        [
-                            contrast_id: 'treatment_mCherry_hND6',
-                            contrast_variable: 'treatment',
-                            contrast_reference: 'mCherry',
-                            contrast_target: 'hND6',
-                            blocking_factors: 'sample_number',
-                            formula: null
-                        ],
+                input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ treatment + (1 | sample_number)'])
+                    .map{
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
+                    }
+
+                input[1] = Channel.of([
+                    [ id:'test' ],
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv", checkIfExists: true),
                         file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv", checkIfExists: true)
                     ]
diff --git a/modules/nf-core/variancepartition/dream/tests/main.nf.test.snap b/modules/nf-core/variancepartition/dream/tests/main.nf.test.snap
index ca054e3fa0f0..34257f3b24d1 100644
--- a/modules/nf-core/variancepartition/dream/tests/main.nf.test.snap
+++ b/modules/nf-core/variancepartition/dream/tests/main.nf.test.snap
@@ -5,10 +5,10 @@
                 "0": [
                     [
                         {
-                            "contrast_id": "treatment_mCherry_hND6",
-                            "contrast_variable": "treatment",
-                            "contrast_reference": "mCherry",
-                            "contrast_target": "hND6",
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
                             "blocking_factors": "sample_number",
                             "formula": "~ treatment + (1 | sample_number)"
                         },
@@ -16,15 +16,41 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking_factors": "sample_number",
+                            "formula": "~ treatment + (1 | sample_number)"
+                        },
+                        "treatment_mCherry_hND6.dream.model.txt:md5,7103206474aa480ffd9cec149263489f"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
                 ],
+                "model": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking_factors": "sample_number",
+                            "formula": "~ treatment + (1 | sample_number)"
+                        },
+                        "treatment_mCherry_hND6.dream.model.txt:md5,7103206474aa480ffd9cec149263489f"
+                    ]
+                ],
                 "results": [
                     [
                         {
-                            "contrast_id": "treatment_mCherry_hND6",
-                            "contrast_variable": "treatment",
-                            "contrast_reference": "mCherry",
-                            "contrast_target": "hND6",
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
                             "blocking_factors": "sample_number",
                             "formula": "~ treatment + (1 | sample_number)"
                         },
@@ -40,7 +66,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-13T14:40:25.867780675"
+        "timestamp": "2025-03-31T15:03:03.556133605"
     },
     "Mus musculus - expression table - contrasts + blocking factors stub": {
         "content": [
@@ -48,28 +74,54 @@
                 "0": [
                     [
                         {
-                            "contrast_id": "treatment_mCherry_hND6",
-                            "contrast_variable": "treatment",
-                            "contrast_reference": "mCherry",
-                            "contrast_target": "hND6",
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
                             "blocking_factors": "sample_number",
-                            "formula": null
+                            "formula": "~ treatment + (1 | sample_number)"
                         },
                         "treatment_mCherry_hND6.dream.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking_factors": "sample_number",
+                            "formula": "~ treatment + (1 | sample_number)"
+                        },
+                        "treatment_mCherry_hND6.dream.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,03b686ec8c67a91501ebb2b2a5234e77"
                 ],
+                "model": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking_factors": "sample_number",
+                            "formula": "~ treatment + (1 | sample_number)"
+                        },
+                        "treatment_mCherry_hND6.dream.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "results": [
                     [
                         {
-                            "contrast_id": "treatment_mCherry_hND6",
-                            "contrast_variable": "treatment",
-                            "contrast_reference": "mCherry",
-                            "contrast_target": "hND6",
+                            "id": "treatment_mCherry_hND6",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
                             "blocking_factors": "sample_number",
-                            "formula": null
+                            "formula": "~ treatment + (1 | sample_number)"
                         },
                         "treatment_mCherry_hND6.dream.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -83,7 +135,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-13T14:40:39.315196311"
+        "timestamp": "2025-03-31T15:03:25.932056996"
     },
     "Mus musculus - expression table - contrasts": {
         "content": [
diff --git a/modules/nf-core/vrhyme/extractunbinned/main.nf b/modules/nf-core/vrhyme/extractunbinned/main.nf
index 0050bb3066d6..7da7e3cfe330 100644
--- a/modules/nf-core/vrhyme/extractunbinned/main.nf
+++ b/modules/nf-core/vrhyme/extractunbinned/main.nf
@@ -9,25 +9,33 @@ process VRHYME_EXTRACTUNBINNED {
 
     input:
     tuple val(meta), path(membership)
-    tuple val(meta), path(fasta)
+    tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path("*_unbinned_sequences.fasta") , emit: unbinned_sequences
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("${prefix}.fasta") , emit: unbinned_sequences
+    path "versions.yml"                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_unbinned_sequences"
+    def fasta_input = fasta.toString().replaceAll(/\.gz$/, '')
+    def gunzip      = fasta.getExtension() == "gz" ? "gunzip -c ${fasta} > ${fasta_input}" : ""
+    def cleanup     = fasta.getExtension() == "gz" ? "rm ${fasta_input}" : ""
+    if( "$fasta_input" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
+    ${gunzip}
+
     extract_unbinned_sequences.py \\
         -i $membership \\
-        -f $fasta \\
-        -o ${prefix}_unbinned_sequences.fasta \\
+        -f $fasta_input \\
+        -o ${prefix}.fasta \\
         $args
 
+    ${cleanup}
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         vrhyme: \$(echo \$(vRhyme --version 2>&1) | sed 's/^.*vRhyme v//; s/Using.*\$//' )
@@ -35,10 +43,11 @@ process VRHYME_EXTRACTUNBINNED {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_unbinned_sequences"
+    def fasta_input = fasta.toString() - ~/\.gz$/
+    if( "$fasta_input" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
-    touch ${prefix}_unbinned_sequences.fasta
+    touch ${prefix}.fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/vrhyme/extractunbinned/meta.yml b/modules/nf-core/vrhyme/extractunbinned/meta.yml
index c9a9b941d595..416798f1add1 100644
--- a/modules/nf-core/vrhyme/extractunbinned/meta.yml
+++ b/modules/nf-core/vrhyme/extractunbinned/meta.yml
@@ -22,21 +22,25 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - membership:
         type: file
         description: TSV file containing information regarding which bins input sequences
           were placed information
         pattern: "*.{tsv}"
-  - - meta:
+        ontologies:
+          - edam: http://edamontology.org/format_3475 # TSV
+  - - meta2:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing information related to the fasta
+          e.g. [ id:'test' ]
     - fasta:
         type: file
         description: FASTA file containing contigs/scaffolds input into vRhyme
-        pattern: "*.{fasta,fna,fa}"
+        pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
 output:
   - unbinned_sequences:
       - meta:
@@ -44,10 +48,12 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*_unbinned_sequences.fasta":
+      - "${prefix}.fasta":
           type: file
           description: FASTA file containing unbinned sequences
           pattern: "*_unbinned_sequences.fasta"
+          ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test
new file mode 100644
index 000000000000..4899735b029f
--- /dev/null
+++ b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test
@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process VRHYME_EXTRACTUNBINNED"
+
+    script "../main.nf"
+    process "VRHYME_EXTRACTUNBINNED"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vrhyme"
+    tag "vrhyme/vrhyme"
+    tag "vrhyme/extractunbinned"
+
+    setup {
+
+        run("VRHYME_VRHYME") {
+            script "../../vrhyme/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+    }
+
+    test("test_vrhyme_extractunbinned") {
+
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.membership
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_vrhyme_extractunbinned -- stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.membership
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test.snap b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test.snap
new file mode 100644
index 000000000000..110efdc2b26d
--- /dev/null
+++ b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "test_vrhyme_extractunbinned -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ],
+                "unbinned_sequences": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-30T20:31:33.979555851"
+    },
+    "test_vrhyme_extractunbinned": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,816e986c8ad8f277eb4a4891a12d7aff"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ],
+                "unbinned_sequences": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,816e986c8ad8f277eb4a4891a12d7aff"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T10:00:14.099653894"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/linkbins/meta.yml b/modules/nf-core/vrhyme/linkbins/meta.yml
index 1302b2ea24fe..ccbb1a401acd 100644
--- a/modules/nf-core/vrhyme/linkbins/meta.yml
+++ b/modules/nf-core/vrhyme/linkbins/meta.yml
@@ -22,7 +22,7 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - bins:
         type: directory
         description: Directory file containing bin FASTA files output by vRhyme (each
@@ -38,11 +38,14 @@ output:
           type: file
           description: FASTA file containing all bins that have been linked by N's
           pattern: "*_linked_bins.fasta"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: []
 authors:
   - "@CarsonJM"
 maintainers:
diff --git a/modules/nf-core/vrhyme/linkbins/tests/main.nf.test b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test
new file mode 100644
index 000000000000..36936f018c17
--- /dev/null
+++ b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test
@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process VRHYME_LINKBINS"
+
+    script "../main.nf"
+    process "VRHYME_LINKBINS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vrhyme"
+    tag "vrhyme/vrhyme"
+    tag "vrhyme/linkbins"
+
+    setup {
+        run("VRHYME_VRHYME") {
+            script "../../vrhyme/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
+                    ]
+                    ]
+				input[1] = [
+				    [ id:'test' ],
+				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+				]
+                """
+            }
+        }
+    }
+
+    test("vrhyme_linkbins") {
+
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.bins
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_vrhyme_linkbins -- stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.bins
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/linkbins/tests/main.nf.test.snap b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test.snap
new file mode 100644
index 000000000000..2ca129f165ca
--- /dev/null
+++ b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "vrhyme_linkbins": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,92cee5d85211d1e657f67ba75d3b2b30"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ],
+                "linked_bins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,92cee5d85211d1e657f67ba75d3b2b30"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T14:18:15.131038697"
+    },
+    "test_vrhyme_linkbins -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ],
+                "linked_bins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T14:18:32.716327779"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/vrhyme/main.nf b/modules/nf-core/vrhyme/vrhyme/main.nf
index 65be074ac8cd..a65788613816 100644
--- a/modules/nf-core/vrhyme/vrhyme/main.nf
+++ b/modules/nf-core/vrhyme/vrhyme/main.nf
@@ -9,7 +9,7 @@ process VRHYME_VRHYME {
 
     input:
     tuple val(meta), path(reads)
-    tuple val(meta), path(fasta)
+    tuple val(meta2), path(fasta)
 
     output:
     tuple val(meta), path("vRhyme_best_bins_fasta/")                , emit: bins
@@ -23,9 +23,14 @@ process VRHYME_VRHYME {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def fasta_input = fasta.toString().replaceAll(/\.gz$/, '')
+    def gunzip      = fasta.getExtension() == "gz" ? "gunzip -c ${fasta} > ${fasta_input}" : ""
+    def cleanup     = fasta.getExtension() == "gz" ? "rm ${fasta_input}" : ""
     """
+    ${gunzip}
+
     vRhyme \\
-        -i $fasta \\
+        -i $fasta_input \\
         -r $reads \\
         -o $prefix \\
         -t $task.cpus \\
@@ -33,6 +38,8 @@ process VRHYME_VRHYME {
 
     mv $prefix/vRhyme_best_bins_fasta/ vRhyme_best_bins_fasta
 
+    ${cleanup}
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         vrhyme: \$(echo \$(vRhyme --version 2>&1) | sed 's/^.*vRhyme v//; s/Using.*\$//' ))
@@ -40,7 +47,6 @@ process VRHYME_VRHYME {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p $prefix
diff --git a/modules/nf-core/vrhyme/vrhyme/meta.yml b/modules/nf-core/vrhyme/vrhyme/meta.yml
index e020a1acde04..b76810fbc4dc 100644
--- a/modules/nf-core/vrhyme/vrhyme/meta.yml
+++ b/modules/nf-core/vrhyme/vrhyme/meta.yml
@@ -22,27 +22,31 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test']
     - reads:
         type: file
         description: Preprocessed FASTQ file containing sample reads
         pattern: "*.{fastq}"
-  - - meta:
+        ontologies:
+          - edam: http://edamontology.org/format_1930 # FASTQ
+  - - meta2:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing fasta information
+          e.g. [ id:'test']
     - fasta:
         type: file
         description: Contigs/scaffolds identified as viral
-        pattern: "*.{fna,fasta,fa}"
+        pattern: "*.{fna,fasta,fa,fasta.gz,fa.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
 output:
   - bins:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - vRhyme_best_bins_fasta/:
           type: directory
           description: Directory containing bin FASTA files
@@ -52,11 +56,13 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test']
       - "**/vRhyme_best_bins.*.membership.tsv":
           type: file
           description: TSV file describing the contig/scaffold membership of each bin
           pattern: "vRhyme_best_bins.*.membership.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
   - summary:
       - meta:
           type: map
@@ -67,11 +73,13 @@ output:
           type: file
           description: TSV file summarizing the attributes of each bin
           pattern: "vRhyme_best_bins.*.summary.tsv"
+          ontologies: []
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: []
 authors:
   - "@CarsonJM"
 maintainers:
diff --git a/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test b/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test
index 5ff7f4e2dc98..57af398ec47d 100644
--- a/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test
+++ b/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test
@@ -10,22 +10,6 @@ nextflow_process {
     tag "modules_vrhyme"
     tag "vrhyme"
     tag "vrhyme/vrhyme"
-    tag "gunzip"
-
-    setup {
-        run("GUNZIP") {
-            script "../../../gunzip/main.nf"
-            process {
-                """
-                input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
-				]
-
-                """
-            }
-        }
-    }
 
     test("test-vrhyme-vrhyme") {
 
@@ -33,14 +17,16 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ],
 				    [
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
 				    ]
 				]
-				input[1] = GUNZIP.out.gunzip
-
+				input[1] = [
+				    [ id:'test', single_end:false ],
+				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+				]
                 """
             }
         }
@@ -65,14 +51,16 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ],
 				    [
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
 				    ]
 				]
-				input[1] = GUNZIP.out.gunzip
-
+				input[1] = [
+				    [ id:'test', single_end:false ],
+				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+				]
                 """
             }
         }
diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf
index 75bea40daf8c..86cc060786ea 100644
--- a/subworkflows/nf-core/abundance_differential_filter/main.nf
+++ b/subworkflows/nf-core/abundance_differential_filter/main.nf
@@ -26,21 +26,22 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     ch_samplesheet           // [ meta_exp, samplesheet ]
     ch_transcript_lengths    // [ meta_exp, transcript_lengths]
     ch_control_features      // [meta_exp, control_features]
-    ch_contrasts             // [[ meta_contrast, contrast_variable, reference, target ]]
-    ch_contrasts_dream       // [meta_contrast, samplesheet, matrix]
+    ch_contrasts             // [[ meta_contrast, contrast_variable, reference, target, formula ]]
 
     main:
 
     ch_versions = Channel.empty()
 
     // Set up how the channels crossed below will be used to generate channels for processing
-    def criteria = multiMapCriteria { meta_input, abundance, analysis_method, fc_threshold, stat_threshold, meta_exp, samplesheet, meta_contrasts, variable, reference, target ->
+    def criteria = multiMapCriteria { meta_input, abundance, analysis_method, fc_threshold, stat_threshold, meta_exp, samplesheet, meta_contrasts, variable, reference, target, formula ->
         def meta_for_diff = mergeMaps(meta_contrasts, meta_input) + [ 'method_differential': analysis_method ]
         def meta_input_new = meta_input + [ 'method_differential': analysis_method ]
         samples_and_matrix:
             [ meta_input_new, samplesheet, abundance ]
         contrasts_for_diff:
             [ meta_for_diff, variable, reference, target ]
+        contrasts_for_diff_with_formula:
+            [ meta_for_diff, variable, reference, target, formula ]
         filter_params:
             [ meta_for_diff, [ 'fc_threshold': fc_threshold, 'stat_threshold': stat_threshold ]]
         contrasts_for_norm:
@@ -131,6 +132,23 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
 
     ch_versions = ch_versions.mix(PROPR_PROPD.out.versions.first())
 
+    // ----------------------------------------------------
+    // Run DREAM
+    // ----------------------------------------------------
+
+    // DREAM only runs with formula
+    dream_inputs = inputs.contrasts_for_diff_with_formula
+        .filter { meta, variable, reference, target, formula ->
+            meta.method_differential == 'dream' && formula != null
+        }
+
+    VARIANCEPARTITION_DREAM(
+        dream_inputs,
+        inputs.samples_and_matrix.filter{ it[0].method_differential == 'dream' }
+    )
+
+    ch_versions = ch_versions.mix( VARIANCEPARTITION_DREAM.out.versions.first() )
+
     // ----------------------------------------------------
     // Collect results
     // ----------------------------------------------------
@@ -138,12 +156,14 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     ch_results = DESEQ2_DIFFERENTIAL.out.results
         .mix(LIMMA_DIFFERENTIAL.out.results)
         .mix(PROPR_PROPD.out.results_genewise)
+        .mix(VARIANCEPARTITION_DREAM.out.results)
 
     ch_normalised_matrix = DESEQ2_NORM.out.normalised_counts
         .mix(LIMMA_NORM.out.normalised_counts)
 
     ch_model = DESEQ2_DIFFERENTIAL.out.model
         .mix(LIMMA_DIFFERENTIAL.out.model)
+        .mix(VARIANCEPARTITION_DREAM.out.model)
 
     ch_variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts
         .mix(DESEQ2_NORM.out.vst_counts)
@@ -168,6 +188,10 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
                 'propd' : [
                     fc_column: 'lfc', fc_cardinality: '>=',
                     stat_column: 'weighted_connectivity', stat_cardinality: '>='
+                ],
+                'dream' : [
+                    fc_column: 'logFC', fc_cardinality: '>=',
+                    stat_column: 'adj.P.Val', stat_cardinality: '<='
                 ]
             ]
             filter_input: [meta + filter_meta, results]
@@ -191,18 +215,10 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
     )
     ch_versions = ch_versions.mix(CUSTOM_FILTERDIFFERENTIALTABLE.out.versions.first())
 
-    ch_dream_results = Channel.empty()
-
-    VARIANCEPARTITION_DREAM(ch_contrasts_dream)
-    ch_versions = ch_versions.mix( VARIANCEPARTITION_DREAM.out.versions.first() )
-    ch_dream_results = VARIANCEPARTITION_DREAM.out.results
-
-
     emit:
     // main results
     results_genewise           = ch_results
     results_genewise_filtered  = CUSTOM_FILTERDIFFERENTIALTABLE.out.filtered
-    results_dream              = ch_dream_results
 
     // pairwise results
     adjacency                  = PROPR_PROPD.out.adjacency
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test
index 7bc99257399a..2d7b968dd60a 100644
--- a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test
+++ b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test
@@ -21,48 +21,30 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                // Define test data
+
                 def testData = [
                     expression_test_data_dir: params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/',
                     contrasts_file: 'SRP254919.contrasts.csv',
-                    samplesheet_file: 'SRP254919.samplesheet.csv',
-                    dream_matrix_file: 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
+                    abundance_file: 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv',
+                    samplesheet_file: 'SRP254919.samplesheet.csv'
                 ]
 
-                // Input (not used)
-                ch_input = Channel.of([
-                    [ id:'test' ],
-                    file(testData.expression_test_data_dir + 'dummy_counts.tsv'),
-                    'dream',  // analysis method
-                    1.5,       // FC threshold
-                    0.05       // stat (adjusted p-value) threshold
-                ])
-
-                // Define additional workflow inputs (not used)
-                ch_samplesheet =  Channel.of([
+                ch_samplesheet = Channel.of([
                     [ id:'test' ],
                     file(testData.expression_test_data_dir + testData.samplesheet_file)
                 ])
                 ch_transcript_lengths = Channel.of([ [], [] ])
                 ch_control_features = Channel.of([ [], [] ])
-                ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
-                    .splitCsv ( header:true, sep:',' )
+                ch_contrasts =  Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ treatment + (1 | sample_number)'])
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
-
-                // Contrasts dream input (used)
-                ch_dream_input = Channel.of([
-                        [   id: 'test',
-                            contrast_id: 'treatment_mCherry_hND6',
-                            contrast_variable: 'treatment',
-                            contrast_reference: 'mCherry',
-                            contrast_target: 'hND6',
-                            blocking_factors: 'sample_number',
-                            formula: '~ treatment + (1 | sample_number)'
-                        ],
-                    file(testData.expression_test_data_dir + testData.samplesheet_file),
-                    file(testData.expression_test_data_dir + testData.dream_matrix_file)
+                ch_input = Channel.of([
+                    [ id:'test' ],
+                    file(testData.expression_test_data_dir + testData.abundance_file),
+                    'dream',  // analysis method
+                    1.5,       // FC threshold
+                    0.05       // stat (adjusted p-value) threshold
                 ])
 
                 input[0] = ch_input
@@ -70,7 +52,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = ch_dream_input
                 """
             }
         }
@@ -78,7 +59,9 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.results_dream,
+                    workflow.out.results_genewise,
+                    workflow.out.results_genewise_filtered,
+                    workflow.out.model,
                     workflow.out.versions
                 ).match() }
             )
@@ -110,7 +93,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -125,7 +108,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
             }
         }
@@ -195,7 +177,7 @@ nextflow_workflow {
                 ch_control_features = Channel.of([ [], [] ])
                 ch_contrasts = Channel.of(['id': 'diagnosis_normal_uremia', 'variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia'])
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = AFFY_JUSTRMA.out.expression.map{ meta, file -> [
                     meta,
@@ -210,8 +192,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
-
                 """
             }
         }
@@ -255,7 +235,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -270,7 +250,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
             }
         }
@@ -317,7 +296,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -332,7 +311,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
             }
         }
@@ -376,7 +354,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -391,7 +369,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
             }
         }
@@ -433,7 +410,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of(
                     [
@@ -457,7 +434,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
             }
         }
@@ -503,7 +479,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of(
                     [
@@ -534,7 +510,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
             }
         }
@@ -583,7 +558,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -598,7 +573,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
             }
         }
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap
index e2dd9c911219..0bd9aedbf07f 100644
--- a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap
@@ -330,18 +330,49 @@
             [
                 [
                     {
-                        "id": "test",
-                        "contrast_id": "treatment_mCherry_hND6",
-                        "contrast_variable": "treatment",
-                        "contrast_reference": "mCherry",
-                        "contrast_target": "hND6",
+                        "id": "treatment_mCherry_hND6_test",
+                        "variable": "treatment",
+                        "reference": "mCherry",
+                        "target": "hND6",
                         "blocking_factors": "sample_number",
-                        "formula": "~ treatment + (1 | sample_number)"
+                        "formula": "~ treatment + (1 | sample_number)",
+                        "method_differential": "dream"
                     },
-                    "treatment_mCherry_hND6.dream.results.tsv:md5,37742ab4ac3152e34339ef423ab1a0a3"
+                    "treatment_mCherry_hND6_test.dream.results.tsv:md5,37742ab4ac3152e34339ef423ab1a0a3"
                 ]
             ],
             [
+                [
+                    {
+                        "id": "treatment_mCherry_hND6_test",
+                        "variable": "treatment",
+                        "reference": "mCherry",
+                        "target": "hND6",
+                        "blocking_factors": "sample_number",
+                        "formula": "~ treatment + (1 | sample_number)",
+                        "method_differential": "dream",
+                        "fc_threshold": 1.5,
+                        "stat_threshold": 0.05
+                    },
+                    "treatment_mCherry_hND6_test_filtered.tsv:md5,9642188f60e8b93abe55a85e99f3dedc"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "treatment_mCherry_hND6_test",
+                        "variable": "treatment",
+                        "reference": "mCherry",
+                        "target": "hND6",
+                        "blocking_factors": "sample_number",
+                        "formula": "~ treatment + (1 | sample_number)",
+                        "method_differential": "dream"
+                    },
+                    "treatment_mCherry_hND6_test.dream.model.txt:md5,7103206474aa480ffd9cec149263489f"
+                ]
+            ],
+            [
+                "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690",
                 "versions.yml:md5,736da31f06f854355d45aeb9d9c874e0"
             ]
         ],
@@ -349,7 +380,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-13T14:51:50.020742089"
+        "timestamp": "2025-03-31T18:16:12.171347414"
     },
     "stub": {
         "content": [
@@ -410,9 +441,6 @@
                     
                 ],
                 "3": [
-                    
-                ],
-                "4": [
                     [
                         {
                             "id": "test",
@@ -421,7 +449,7 @@
                         "test.normalised_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "5": [
+                "4": [
                     [
                         {
                             "id": "test",
@@ -432,7 +460,7 @@
                         ]
                     ]
                 ],
-                "6": [
+                "5": [
                     [
                         {
                             "id": "treatment_mCherry_hND6__test",
@@ -456,7 +484,7 @@
                         "treatment_mCherry_hND6_sample_number_test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "7": [
+                "6": [
                     "versions.yml:md5,05e3901f6d78f8839a7e07f422e9bc03",
                     "versions.yml:md5,1d567f203085b6ae7b621d5587260a23",
                     "versions.yml:md5,50cd86004ca6259274b10316b1b96f00"
@@ -496,9 +524,6 @@
                         },
                         "test.normalised_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "results_dream": [
-                    
                 ],
                 "results_genewise": [
                     [
@@ -574,7 +599,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-11T17:52:36.213485364"
+        "timestamp": "2025-03-31T18:43:26.944581418"
     },
     "deseq2 - mouse - basic": {
         "content": [
diff --git a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test
index 9d06145068d4..8aabc9bfbf66 100644
--- a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test
+++ b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test
@@ -10,6 +10,9 @@ nextflow_workflow {
     tag "samtools"
     tag "samtools/sort"
     tag "samtools/index"
+    tag "ngscheckmate/ncm"
+    tag "bcftools/mpileup"
+
     config "./nextflow.config"
 
     test("sarscov2 - bam") {
@@ -46,7 +49,7 @@ nextflow_workflow {
                 { assert workflow.success},
                 { assert snapshot(
                     workflow.out.corr_matrix,
-                    workflow.out.matched,
+                    file(workflow.out.matched[0][1]).name,
                     workflow.out.all,
                     workflow.out.vcf.collect {meta, vcf -> path(vcf).vcf.variantsMD5 },
                     file(workflow.out.pdf[0][1]).name,
@@ -129,7 +132,14 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match()}
+                { assert snapshot(
+                    file(workflow.out.corr_matrix[0][1]).name,
+                    file(workflow.out.matched[0][1]).name,
+                    file(workflow.out.all[0][1]).name,
+                    // workflow.out.vcf.collect {meta, vcf -> path(vcf).vcf.variantsMD5 },
+                    file(workflow.out.pdf[0][1]).name,
+                    workflow.out.versions
+                    ).match()}
             )
         }
     }
diff --git a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap
index f1cfed35c836..872274ec580a 100644
--- a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap
@@ -1,116 +1,21 @@
 {
     "sarscov2 - bam - stub": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed_output_corr_matrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed_matched.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed_all.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test1"
-                        },
-                        "test1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ],
-                    [
-                        {
-                            "id": "test2"
-                        },
-                        "test2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "4": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "5": [
-                    "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab",
-                    "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb",
-                    "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb"
-                ],
-                "all": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed_all.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "corr_matrix": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed_output_corr_matrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "matched": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed_matched.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "pdf": [
-                    [
-                        {
-                            "id": "test_bed"
-                        },
-                        "test_bed.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test1"
-                        },
-                        "test1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ],
-                    [
-                        {
-                            "id": "test2"
-                        },
-                        "test2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab",
-                    "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb",
-                    "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb"
-                ]
-            }
+            "test_bed_output_corr_matrix.txt",
+            "test_bed_matched.txt",
+            "test_bed_all.txt",
+            "test_bed.pdf",
+            [
+                "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab",
+                "versions.yml:md5,d0f4716ff5035090e3129d50d029e7c8",
+                "versions.yml:md5,d0f4716ff5035090e3129d50d029e7c8"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-03T07:29:50.686838875"
+        "timestamp": "2025-04-01T17:50:34.789565772"
     },
     "sarscov2 - cram": {
         "content": [
@@ -139,21 +44,21 @@
                 ]
             ],
             [
-                "1ab17b219dbcd4b760b1e19f1cf3f154",
-                "fd5de4fc04e60573b4557531fbb8ef15"
+                "d5b1e887b104cd33f18747abd377f47a",
+                "30feeb598a3730af169e3d14c56a05c2"
             ],
             "test_bed.pdf",
             [
                 "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab",
-                "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb",
-                "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb"
+                "versions.yml:md5,d0f4716ff5035090e3129d50d029e7c8",
+                "versions.yml:md5,d0f4716ff5035090e3129d50d029e7c8"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-05T15:06:58.780928754"
+        "timestamp": "2025-04-01T16:46:55.771293323"
     },
     "sarscov2 - bam": {
         "content": [
@@ -165,14 +70,7 @@
                     "test_bed_output_corr_matrix.txt:md5,3a23347ff7071d5d8e273bfc29731d4a"
                 ]
             ],
-            [
-                [
-                    {
-                        "id": "test_bed"
-                    },
-                    "test_bed_matched.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
+            "test_bed_matched.txt",
             [
                 [
                     {
@@ -182,20 +80,20 @@
                 ]
             ],
             [
-                "748c1158a2e2341c80082fd467ff3e3b",
-                "7aeb02c2ee40182485f619406e2bfb24"
+                "9341ed6b9cca02d6b0b822308f4a48c6",
+                "3d6ba59b24dc0a699d9bd5a78bc76869"
             ],
             "test_bed.pdf",
             [
                 "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab",
-                "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb",
-                "versions.yml:md5,ef35c999cb0eaf32e3a167021fde5acb"
+                "versions.yml:md5,d0f4716ff5035090e3129d50d029e7c8",
+                "versions.yml:md5,d0f4716ff5035090e3129d50d029e7c8"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-05T15:06:44.703957197"
+        "timestamp": "2025-04-01T17:45:22.458317234"
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test.snap b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test.snap
index c16d8793d08b..2e18e624f0fe 100644
--- a/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test.snap
@@ -12,16 +12,16 @@
                 ]
             ],
             [
-                "versions.yml:md5,d3e911c025e35de092f7ef0073ccf807",
-                "versions.yml:md5,df54ea89f3bcb7e5952e7e3dae1d22a4",
-                "versions.yml:md5,e66aeb30f8646d583bec6fbf4fe02426"
+                "versions.yml:md5,3058c750cfdd13e5c2448debfb2d1029",
+                "versions.yml:md5,67aa350d7830af571a7e9fd507fd53ec",
+                "versions.yml:md5,ee7a7985addc258263151e82e6fc90e8"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-02T16:12:55.505491641"
+        "timestamp": "2025-04-01T16:11:46.751764888"
     },
     "sarscov2 - bam - skip - val - nodb": {
         "content": [
@@ -36,16 +36,16 @@
                 ]
             ],
             [
-                "versions.yml:md5,4b7dccb03c75e8e94d7c6bdefaa90c95",
-                "versions.yml:md5,df54ea89f3bcb7e5952e7e3dae1d22a4",
-                "versions.yml:md5,e66aeb30f8646d583bec6fbf4fe02426"
+                "versions.yml:md5,3058c750cfdd13e5c2448debfb2d1029",
+                "versions.yml:md5,670c845058d3da5dac16f65c7a53ee34",
+                "versions.yml:md5,67aa350d7830af571a7e9fd507fd53ec"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-02T16:13:29.413908034"
+        "timestamp": "2025-04-01T16:12:02.32769656"
     },
     "sarscov2 - bam - val - nodb": {
         "content": [
@@ -60,16 +60,16 @@
                 ]
             ],
             [
-                "versions.yml:md5,4b7dccb03c75e8e94d7c6bdefaa90c95",
-                "versions.yml:md5,d3e911c025e35de092f7ef0073ccf807",
-                "versions.yml:md5,df54ea89f3bcb7e5952e7e3dae1d22a4",
-                "versions.yml:md5,e66aeb30f8646d583bec6fbf4fe02426"
+                "versions.yml:md5,3058c750cfdd13e5c2448debfb2d1029",
+                "versions.yml:md5,670c845058d3da5dac16f65c7a53ee34",
+                "versions.yml:md5,67aa350d7830af571a7e9fd507fd53ec",
+                "versions.yml:md5,ee7a7985addc258263151e82e6fc90e8"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-02T16:12:09.796799525"
+        "timestamp": "2025-04-01T16:11:21.971966389"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/differential_functional_enrichment/main.nf b/subworkflows/nf-core/differential_functional_enrichment/main.nf
index 802812a5d938..e219a7d0dafc 100644
--- a/subworkflows/nf-core/differential_functional_enrichment/main.nf
+++ b/subworkflows/nf-core/differential_functional_enrichment/main.nf
@@ -26,7 +26,7 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT {
     // other - for the moment these files are only needed for GSEA
     // as it is the only one that takes expression data as input
     // if in the future this setting is changed, this section could be removed
-    ch_contrasts             // [ meta_contrast, contrast_variable, reference, target ]
+    ch_contrasts             // [ meta_contrast, contrast_variable, reference, target, formula ]
     ch_samplesheet           // [ meta_exp, samples sheet ]
     ch_featuresheet          // [ meta_exp, features sheet, features id, features symbol ]
 
@@ -53,7 +53,7 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT {
     // In the case of GSEA, it needs additional files coming from other channels that other methods don't use
     // here we define the input channel for the GSEA section
 
-    def criteria = multiMapCriteria { meta_input, input, genesets, meta_exp, samplesheet, featuresheet, features_id, features_symbol, meta_contrasts, variable, reference, target ->
+    def criteria = multiMapCriteria { meta_input, input, genesets, meta_exp, samplesheet, featuresheet, features_id, features_symbol, meta_contrasts, variable, reference, target, _formula ->
         def meta_contrasts_new = meta_contrasts + [ 'variable': variable, 'reference': reference, 'target': target ]  // make sure variable, reference, target are in the meta
         def meta_all = mergeMaps(meta_contrasts_new, meta_input)
         input:
diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test
index d71e7a508eb0..145688c46687 100644
--- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test
+++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test
@@ -37,7 +37,7 @@ nextflow_workflow {
                 ])
 
                 input[0] = ch_input
-                input[1] = Channel.of([[], [], [], []])
+                input[1] = Channel.of([[], [], [], [], []])
                 input[2] = Channel.of([[], []])
                 input[3] = Channel.of([[], [], [], []])
                 """
@@ -85,7 +85,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -100,7 +100,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
                 }
             }
@@ -115,7 +114,7 @@ nextflow_workflow {
                     }
 
                 input[0] = ch_input
-                input[1] = Channel.of([[], [], [], []])
+                input[1] = Channel.of([[], [], [], [], []])
                 input[2] = Channel.of([[], []])
                 input[3] = Channel.of([[], [], [], []])
                 """
@@ -163,7 +162,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -178,7 +177,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
                 }
             }
@@ -205,7 +203,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_samplesheet = Channel.of([
                     [ id:'test' ],
@@ -265,7 +263,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of([
                     [ id:'test' ],
@@ -280,7 +278,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
                 }
             }
@@ -296,7 +293,7 @@ nextflow_workflow {
                     }
 
                 input[0] = ch_input
-                input[1] = Channel.of([[], [], [], []])
+                input[1] = Channel.of([[], [], [], [], []])
                 input[2] = Channel.of([[], []])
                 input[3] = Channel.of([[], [], [], []])
                 """
@@ -342,7 +339,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.expression_test_data_dir + testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_input = Channel.of(
                     [
@@ -373,7 +370,6 @@ nextflow_workflow {
                 input[2] = ch_transcript_lengths
                 input[3] = ch_control_features
                 input[4] = ch_contrasts
-                input[5] = Channel.empty()
                 """
                 }
             }
@@ -410,7 +406,7 @@ nextflow_workflow {
                 ch_contrasts = Channel.fromPath(file(testData.contrasts_file))
                     .splitCsv ( header:true, sep:',' )
                     .map{
-                        tuple(it, it.variable, it.reference, it.target)
+                        tuple(it, it.variable, it.reference, it.target, it.formula)
                     }
                 ch_samplesheet = Channel.of([
                     [ id:'test' ],
@@ -464,7 +460,7 @@ nextflow_workflow {
                 ])
 
                 input[0] = ch_input
-                input[1] = Channel.of([[], [], [], []])
+                input[1] = Channel.of([[], [], [], [], []])
                 input[2] = Channel.of([[], []])
                 input[3] = Channel.of([[], [], [], []])
                 """
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
index 1c3ef6b9e20f..c385612f792e 100644
--- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
@@ -153,7 +153,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
         )
         ch_versions = ch_versions.mix(FQ_LINT.out.versions.first())
         ch_lint_log = ch_lint_log.mix(FQ_LINT.out.lint)
-        ch_filtered_reads = ch_reads.join(FQ_LINT.out.lint.map{it[0]})
+        ch_filtered_reads = ch_filtered_reads.join(FQ_LINT.out.lint.map{it[0]})
     }
 
     //
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
index b338fbc9d6c7..ba4bf68782db 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
@@ -49,10 +49,10 @@
                 "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
                 "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
                 "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
-                "versions.yml:md5,47202c93baf73d3ad45971e632e6ba28",
-                "versions.yml:md5,47202c93baf73d3ad45971e632e6ba28",
-                "versions.yml:md5,47202c93baf73d3ad45971e632e6ba28",
-                "versions.yml:md5,47202c93baf73d3ad45971e632e6ba28",
+                "versions.yml:md5,2da388fbfa046fb49d5b7475946565ab",
+                "versions.yml:md5,2da388fbfa046fb49d5b7475946565ab",
+                "versions.yml:md5,2da388fbfa046fb49d5b7475946565ab",
+                "versions.yml:md5,2da388fbfa046fb49d5b7475946565ab",
                 "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
                 "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
                 "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
@@ -61,17 +61,17 @@
                 "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
                 "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
                 "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
-                "versions.yml:md5,8c6ce76e0c02205fc17bce7b86ecc135",
-                "versions.yml:md5,8c6ce76e0c02205fc17bce7b86ecc135",
-                "versions.yml:md5,8c6ce76e0c02205fc17bce7b86ecc135",
-                "versions.yml:md5,8c6ce76e0c02205fc17bce7b86ecc135"
+                "versions.yml:md5,f9cf90f8bc8666204dd170f9c3394a03",
+                "versions.yml:md5,f9cf90f8bc8666204dd170f9c3394a03",
+                "versions.yml:md5,f9cf90f8bc8666204dd170f9c3394a03",
+                "versions.yml:md5,f9cf90f8bc8666204dd170f9c3394a03"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-01T13:00:44.890381019"
+        "timestamp": "2025-04-01T13:30:02.259419945"
     },
     "merged": {
         "content": [
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index 9beb754e7374..f279a62e190d 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -7,8 +7,8 @@ params {
 
 process {
     resourceLimits = [
-        cpus: 2,
-        memory: '4.GB',
+        cpus: 4,
+        memory: '16.GB',
         time: '1.h'
     ]
 }
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 3449f48a2bfa..48980a313e56 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1,16 +1,6 @@
-cellrangerarc/count:
-  - modules/nf-core/cellrangerarc/count/**
-  - tests/modules/nf-core/cellrangerarc/count/**
-  - modules/nf-core/cellrangerarc/mkref/**
-  - tests/modules/nf-core/cellrangerarc/mkref/**
 cellrangerarc/mkfastq:
   - modules/nf-core/cellrangerarc/mkfastq/**
   - tests/modules/nf-core/cellrangerarc/mkfastq/**
-cellrangerarc/mkref:
-  - modules/nf-core/cellrangerarc/mkref/**
-  - tests/modules/nf-core/cellrangerarc/mkref/**
-  - modules/nf-core/cellrangerarc/mkgtf/**
-  - tests/modules/nf-core/cellrangerarc/mkgtf/**
 cellrangeratac/count:
   - modules/nf-core/cellrangeratac/count/**
   - tests/modules/nf-core/cellrangeratac/count/**
@@ -22,33 +12,12 @@ cellrangeratac/mkfastq:
 cellrangeratac/mkref:
   - modules/nf-core/cellrangeratac/mkref/**
   - tests/modules/nf-core/cellrangeratac/mkref/**
-damageprofiler:
-  - modules/nf-core/damageprofiler/**
-  - tests/modules/nf-core/damageprofiler/**
-fcs/fcsgx:
-  - modules/nf-core/fcs/fcsgx/**
-  - tests/modules/nf-core/fcs/fcsgx/**
 gangstr:
   - modules/nf-core/gangstr/**
   - tests/modules/nf-core/gangstr/**
 gatk/indelrealigner:
   - modules/nf-core/gatk/indelrealigner/**
   - tests/modules/nf-core/gatk/indelrealigner/**
-gem2/gem2bedmappability:
-  - modules/nf-core/gem2/gem2bedmappability/**
-  - tests/modules/nf-core/gem2/gem2bedmappability/**
-gem2/gemmappability:
-  - modules/nf-core/gem2/gemmappability/**
-  - tests/modules/nf-core/gem2/gemmappability/**
-genescopefk:
-  - modules/nf-core/genescopefk/**
-  - tests/modules/nf-core/genescopefk/**
-genmap/map:
-  - modules/nf-core/genmap/map/**
-  - tests/modules/nf-core/genmap/map/**
-genotyphi/parse:
-  - modules/nf-core/genotyphi/parse/**
-  - tests/modules/nf-core/genotyphi/parse/**
 gget/gget:
   - modules/nf-core/gget/gget/**
   - tests/modules/nf-core/gget/gget/**
@@ -154,9 +123,6 @@ paragraph/multigrmpy:
 phyloflash:
   - modules/nf-core/phyloflash/**
   - tests/modules/nf-core/phyloflash/**
-plink/indeppairwise:
-  - modules/nf-core/plink/indeppairwise/**
-  - tests/modules/nf-core/plink/indeppairwise/**
 pneumocat:
   - modules/nf-core/pneumocat/**
   - tests/modules/nf-core/pneumocat/**
@@ -206,9 +172,6 @@ sgdemux:
   - modules/nf-core/sgdemux/**
   - modules/nf-core/untar/**
   - tests/modules/nf-core/sgdemux/**
-shigeifinder:
-  - modules/nf-core/shigeifinder/**
-  - tests/modules/nf-core/shigeifinder/**
 somalier/ancestry:
   - modules/nf-core/somalier/ancestry/**
   - tests/modules/nf-core/somalier/ancestry/**
@@ -218,9 +181,6 @@ spatyper:
 srst2/srst2:
   - modules/nf-core/srst2/srst2/**
   - tests/modules/nf-core/srst2/srst2/**
-stecfinder:
-  - modules/nf-core/stecfinder/**
-  - tests/modules/nf-core/stecfinder/**
 subworkflows/bam_cnv_wisecondorx:
   - subworkflows/nf-core/bam_cnv_wisecondorx/**
   - tests/subworkflows/nf-core/bam_cnv_wisecondorx/**
@@ -275,30 +235,24 @@ subworkflows/vcf_gather_bcftools:
 subworkflows/vcf_phase_shapeit5:
   - subworkflows/nf-core/vcf_phase_shapeit5/**
   - tests/subworkflows/nf-core/vcf_phase_shapeit5/**
-survivor/filter:
-  - modules/nf-core/survivor/filter/**
-  - tests/modules/nf-core/survivor/filter/**
-survivor/simsv:
-  - modules/nf-core/survivor/simsv/**
-  - tests/modules/nf-core/survivor/simsv/**
 svaba:
   - modules/nf-core/svaba/**
   - tests/modules/nf-core/svaba/**
 svtk/baftest:
   - modules/nf-core/svtk/baftest/**
   - tests/modules/nf-core/svtk/baftest/**
-svtk/rdtest2vcf:
-  - modules/nf-core/svtk/rdtest2vcf/**
-  - tests/modules/nf-core/svtk/rdtest2vcf/**
-svtk/standardize:
-  - modules/nf-core/svtk/standardize/**
-  - tests/modules/nf-core/svtk/standardize/**
+topas/gencons:
+  - modules/nf-core/topas/gencons/**
+  - tests/modules/nf-core/topas/gencons/**
 truvari/bench:
   - modules/nf-core/truvari/bench/**
   - tests/modules/nf-core/truvari/bench/**
 ultra/align:
   - modules/nf-core/ultra/align/**
   - tests/modules/nf-core/ultra/align/**
+ultra/index:
+  - modules/nf-core/ultra/index/**
+  - tests/modules/nf-core/ultra/index/**
 universc:
   - modules/nf-core/universc/**
   - tests/modules/nf-core/universc/**
@@ -308,9 +262,3 @@ varlociraptor/callvariants:
 varlociraptor/preprocess:
   - modules/nf-core/varlociraptor/preprocess/**
   - tests/modules/nf-core/varlociraptor/preprocess/**
-vrhyme/extractunbinned:
-  - modules/nf-core/vrhyme/extractunbinned/**
-  - tests/modules/nf-core/vrhyme/extractunbinned/**
-vrhyme/linkbins:
-  - modules/nf-core/vrhyme/linkbins/**
-  - tests/modules/nf-core/vrhyme/linkbins/**
diff --git a/tests/modules/nf-core/cellrangerarc/count/main.nf b/tests/modules/nf-core/cellrangerarc/count/main.nf
deleted file mode 100644
index dca5ded3a4de..000000000000
--- a/tests/modules/nf-core/cellrangerarc/count/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CELLRANGERARC_MKREF } from '../../../../../modules/nf-core/cellrangerarc/mkref/main.nf'
-include { CELLRANGERARC_COUNT } from '../../../../../modules/nf-core/cellrangerarc/count/main.nf'
-include { UNZIP } from '../../../../../modules/nf-core/unzip/main.nf'
-
-workflow test_cellrangerarc_count {
-
-    input = [ [ id:'test' ], [ 'gex','atac' ], [ 'SRR18907480_chr19_sub','SRR18907481_chr19_sub' ],
-            [  file(params.test_data['mus_musculus']['illumina']['test_scARC_gex_R1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['mus_musculus']['illumina']['test_scARC_gex_R2_fastq_gz'], checkIfExists: true),
-                file(params.test_data['mus_musculus']['illumina']['test_scARC_atac_R1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['mus_musculus']['illumina']['test_scARC_atac_R2_fastq_gz'], checkIfExists: true),
-                file(params.test_data['mus_musculus']['illumina']['test_scARC_atac_I2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    fasta = [ [], file(params.test_data['mus_musculus']['genome']['genome_19_fasta'], checkIfExists: true)]
-    gtf = file(params.test_data['mus_musculus']['genome']['genome_19_gtf'], checkIfExists: true)
-    motifs = file(params.test_data['homo_sapiens']['genome']['genome_motifs'], checkIfExists: true)
-    reference_config = file(params.test_data['mus_musculus']['illumina']['genome_config'], checkIfExists: true)
-    reference_name = "cellrangerarc_reference"
-    lib_csv = file(params.test_data['mus_musculus']['illumina']['multiome_lib_csv'], checkIfExists: true)
-
-    UNZIP( fasta )
-
-    CELLRANGERARC_MKREF ( UNZIP.out.unzipped_archive.map{ it[1] } + "/chr19.fa",
-                            gtf,
-                            motifs,
-                            reference_config,
-                            reference_name )
-
-    CELLRANGERARC_COUNT(
-        input,
-        CELLRANGERARC_MKREF.out.reference
-    )
-}
diff --git a/tests/modules/nf-core/cellrangerarc/count/nextflow.config b/tests/modules/nf-core/cellrangerarc/count/nextflow.config
deleted file mode 100644
index 1df91eee5da5..000000000000
--- a/tests/modules/nf-core/cellrangerarc/count/nextflow.config
+++ /dev/null
@@ -1,27 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: CELLRANGERARC_MKGTF {
-        ext.args = '--attribute=gene_biotype:protein_coding \
-            --attribute=gene_biotype:lincRNA \
-            --attribute=gene_biotype:antisense \
-            --attribute=gene_biotype:IG_LV_gene \
-            --attribute=gene_biotype:IG_V_gene \
-            --attribute=gene_biotype:IG_V_pseudogene \
-            --attribute=gene_biotype:IG_D_gene \
-            --attribute=gene_biotype:IG_J_gene \
-            --attribute=gene_biotype:IG_J_pseudogene \
-            --attribute=gene_biotype:IG_C_gene \
-            --attribute=gene_biotype:IG_C_pseudogene \
-            --attribute=gene_biotype:TR_V_gene \
-            --attribute=gene_biotype:TR_V_pseudogene \
-            --attribute=gene_biotype:TR_D_gene \
-            --attribute=gene_biotype:TR_J_gene \
-            --attribute=gene_biotype:TR_J_pseudogene \
-            --attribute=gene_biotype:TR_C_gene'
-
-
-    }
-
-}
diff --git a/tests/modules/nf-core/cellrangerarc/count/test.yml b/tests/modules/nf-core/cellrangerarc/count/test.yml
deleted file mode 100644
index c94c786fbbbb..000000000000
--- a/tests/modules/nf-core/cellrangerarc/count/test.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-- name: cellrangerarc_count test_cellrangerarc_count
-  command: nextflow run ./tests/modules/nf-core/cellrangerarc/count -entry test_cellrangerarc_count -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cellrangerarc/count/nextflow.config
-  tags:
-    - cellrangerarc/count
-    - cellrangerarc
-  files:
-    - path: output/cellrangerarc/cellrangerarc_reference/fasta/genome.fa
-      md5sum: dd9375c0cfa5de18757a0608411ff608
-    - path: output/cellrangerarc/cellrangerarc_reference/fasta/genome.fa.fai
-      md5sum: 291a00d5431e0f97c356c272d201d8bd
-    - path: output/cellrangerarc/cellrangerarc_reference/genes/genes.gtf.gz
-      md5sum: f9fc85cbe202ecd716f05f16a352ce19
-    - path: output/cellrangerarc/cellrangerarc_reference/reference.json
-      md5sum: 1ff977fa99515695d81b8da012569901
-    - path: output/cellrangerarc/cellrangerarc_reference/regions/motifs.pfm
-      md5sum: 294d4041e4ffd4c633376c2b9d180ac0
-    - path: output/cellrangerarc/cellrangerarc_reference/regions/transcripts.bed
-      md5sum: bc5cfb75dc1795cfc2caeddfc15aaa30
-    - path: output/cellrangerarc/cellrangerarc_reference/regions/tss.bed
-      md5sum: 6aa464a762cab3ca3bf004dd6f35de8e
-    - path: output/cellrangerarc/test/outs/filtered_feature_bc_matrix.h5
-    - path: output/cellrangerarc/test/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
-    - path: output/cellrangerarc/test/outs/filtered_feature_bc_matrix/features.tsv.gz
-    - path: output/cellrangerarc/test/outs/filtered_feature_bc_matrix/matrix.mtx.gz
-    - path: output/cellrangerarc/test/outs/summary.csv
-      md5sum: 7641192d4cc0c6072dc447a46d5f89a2
-    - path: output/cellrangerarc/test/outs/gex_possorted_bam.bam
-      md5sum: 8455846fa1aa417e4252bd09584d1098
-    - path: output/cellrangerarc/test/outs/gex_possorted_bam.bam.bai
-      md5sum: 444fb175b75d0e22c8e14724b7790e34
-    - path: output/cellrangerarc/test/outs/raw_feature_bc_matrix.h5
-    - path: output/cellrangerarc/test/outs/raw_feature_bc_matrix/barcodes.tsv.gz
-    - path: output/cellrangerarc/test/outs/raw_feature_bc_matrix/features.tsv.gz
-    - path: output/cellrangerarc/test/outs/raw_feature_bc_matrix/matrix.mtx.gz
-    - path: output/cellrangerarc/test/outs/atac_peaks.bed
-    - path: output/cellrangerarc/test/outs/atac_possorted_bam.bam
-    - path: output/cellrangerarc/test/outs/atac_possorted_bam.bam.bai
-    - path: output/cellrangerarc/test/outs/web_summary.html
diff --git a/tests/modules/nf-core/cellrangerarc/mkref/main.nf b/tests/modules/nf-core/cellrangerarc/mkref/main.nf
deleted file mode 100644
index 90a3534f5431..000000000000
--- a/tests/modules/nf-core/cellrangerarc/mkref/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CELLRANGERARC_MKREF } from '../../../../../modules/nf-core/cellrangerarc/mkref/main.nf'
-include { UNZIP } from '../../../../../modules/nf-core/unzip/main.nf'
-
-workflow test_cellrangerarc_mkref {
-
-    fasta = [ [], file(params.test_data['mus_musculus']['genome']['genome_19_fasta'], checkIfExists: true)]
-    gtf = file(params.test_data['mus_musculus']['genome']['genome_19_gtf'], checkIfExists: true)
-    motifs = file(params.test_data['homo_sapiens']['genome']['genome_motifs'], checkIfExists: true)
-    reference_config = file(params.test_data['mus_musculus']['illumina']['genome_config'], checkIfExists: true)
-    reference_name = "cellrangerarc_reference"
-
-    UNZIP( fasta )
-
-    CELLRANGERARC_MKREF ( UNZIP.out.unzipped_archive.map{ it[1] } + "/chr19.fa",
-                            gtf,
-                            motifs,
-                            reference_config,
-                            reference_name )
-}
diff --git a/tests/modules/nf-core/cellrangerarc/mkref/nextflow.config b/tests/modules/nf-core/cellrangerarc/mkref/nextflow.config
deleted file mode 100644
index 8730f1c4b930..000000000000
--- a/tests/modules/nf-core/cellrangerarc/mkref/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/cellrangerarc/mkref/test.yml b/tests/modules/nf-core/cellrangerarc/mkref/test.yml
deleted file mode 100644
index 2e631f7cb8af..000000000000
--- a/tests/modules/nf-core/cellrangerarc/mkref/test.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-- name: cellrangerarc_mkref test_cellrangerarc_mkref
-  command: nextflow run ./tests/modules/nf-core/cellrangerarc/mkref -entry test_cellrangerarc_mkref -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cellrangerarc/mkref/nextflow.config
-  tags:
-    - cellrangerarc/mkref
-    - cellrangerarc
-  files:
-    - path: output/cellrangerarc/cellrangerarc_reference/fasta/genome.fa
-      md5sum: dd9375c0cfa5de18757a0608411ff608
-    - path: output/cellrangerarc/cellrangerarc_reference/fasta/genome.fa.fai
-      md5sum: 291a00d5431e0f97c356c272d201d8bd
-    - path: output/cellrangerarc/cellrangerarc_reference/genes/genes.gtf.gz
-      md5sum: f9fc85cbe202ecd716f05f16a352ce19
-    - path: output/cellrangerarc/cellrangerarc_reference/reference.json
-      md5sum: 1ff977fa99515695d81b8da012569901
-    - path: output/cellrangerarc/cellrangerarc_reference/regions/motifs.pfm
-      md5sum: 294d4041e4ffd4c633376c2b9d180ac0
-    - path: output/cellrangerarc/cellrangerarc_reference/regions/transcripts.bed
-      md5sum: bc5cfb75dc1795cfc2caeddfc15aaa30
-    - path: output/cellrangerarc/cellrangerarc_reference/regions/tss.bed
-      md5sum: 6aa464a762cab3ca3bf004dd6f35de8e
diff --git a/tests/modules/nf-core/damageprofiler/main.nf b/tests/modules/nf-core/damageprofiler/main.nf
deleted file mode 100644
index 128bc52124f9..000000000000
--- a/tests/modules/nf-core/damageprofiler/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DAMAGEPROFILER } from '../../../../modules/nf-core/damageprofiler/main.nf'
-
-workflow test_damageprofiler {
-
-    input        = [ [ id:'test', single_end:false ], // meta map
-                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
-    fasta        = []
-    fai          = []
-    species_list = []
-
-
-    DAMAGEPROFILER ( input, fasta, fai, species_list )
-}
-
-workflow test_damageprofiler_reference {
-
-    input        = [ [ id:'test', single_end:false ], // meta map
-                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
-    fasta        = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai          = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    species_list = []
-
-    DAMAGEPROFILER ( input, fasta, fai, species_list )
-}
-
-workflow test_damageprofiler_specieslist {
-
-    input        = [ [ id:'test', single_end:false ], // meta map
-                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
-    fasta        = []
-    fai          = []
-    species_list = file(params.test_data['homo_sapiens']['genome']['genome_header'], checkIfExists: true)
-
-    DAMAGEPROFILER ( input, fasta, fai, species_list )
-}
diff --git a/tests/modules/nf-core/damageprofiler/nextflow.config b/tests/modules/nf-core/damageprofiler/nextflow.config
deleted file mode 100644
index 8730f1c4b930..000000000000
--- a/tests/modules/nf-core/damageprofiler/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/damageprofiler/test.yml b/tests/modules/nf-core/damageprofiler/test.yml
deleted file mode 100644
index bbaa31c0f825..000000000000
--- a/tests/modules/nf-core/damageprofiler/test.yml
+++ /dev/null
@@ -1,77 +0,0 @@
-- name: damageprofiler test_damageprofiler
-  command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/damageprofiler/nextflow.config
-  tags:
-    - damageprofiler
-  files:
-    - path: output/damageprofiler/test/3pGtoA_freq.txt
-      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
-    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
-      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
-    - path: output/damageprofiler/test/5pCtoT_freq.txt
-      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
-    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
-      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
-    - path: output/damageprofiler/test/DNA_comp_genome.txt
-      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
-    - path: output/damageprofiler/test/DNA_composition_sample.txt
-      md5sum: 16be9c91a06fa7defee376230b12862f
-    - path: output/damageprofiler/test/DamagePlot.pdf
-    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
-    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
-    - path: output/damageprofiler/test/DamageProfiler.log
-    - path: output/damageprofiler/test/Length_plot.pdf
-    - path: output/damageprofiler/test/Length_plot_combined_data.svg
-    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
-    - path: output/damageprofiler/test/dmgprof.json
-      md5sum: a011a47edaadb3a07527c329a6492570
-    - path: output/damageprofiler/test/editDistance.txt
-      md5sum: 7590dac007633ee11025cc99ec9f009b
-    - path: output/damageprofiler/test/edit_distance.pdf
-    - path: output/damageprofiler/test/edit_distance.svg
-    - path: output/damageprofiler/test/lgdistribution.txt
-      md5sum: 583fd98094de3fb462b133daeaadcf52
-    - path: output/damageprofiler/test/misincorporation.txt
-      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
-
-- name: damageprofiler test_damageprofiler_reference
-  command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/damageprofiler/nextflow.config
-  tags:
-    - damageprofiler
-  files:
-    - path: output/damageprofiler/test/3pGtoA_freq.txt
-      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
-    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
-      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
-    - path: output/damageprofiler/test/5pCtoT_freq.txt
-      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
-    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
-      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
-    - path: output/damageprofiler/test/DNA_comp_genome.txt
-      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
-    - path: output/damageprofiler/test/DNA_composition_sample.txt
-      md5sum: 16be9c91a06fa7defee376230b12862f
-    - path: output/damageprofiler/test/DamagePlot.pdf
-    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
-    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
-    - path: output/damageprofiler/test/DamageProfiler.log
-    - path: output/damageprofiler/test/Length_plot.pdf
-    - path: output/damageprofiler/test/Length_plot_combined_data.svg
-    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
-    - path: output/damageprofiler/test/dmgprof.json
-      md5sum: a011a47edaadb3a07527c329a6492570
-    - path: output/damageprofiler/test/editDistance.txt
-      md5sum: 7590dac007633ee11025cc99ec9f009b
-    - path: output/damageprofiler/test/edit_distance.pdf
-    - path: output/damageprofiler/test/edit_distance.svg
-    - path: output/damageprofiler/test/lgdistribution.txt
-      md5sum: 583fd98094de3fb462b133daeaadcf52
-    - path: output/damageprofiler/test/misincorporation.txt
-      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
-
-- name: damageprofiler test_damageprofiler_specieslist
-  command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/damageprofiler/nextflow.config
-  tags:
-    - damageprofiler
-  files:
-    - path: output/damageprofiler/test/DamageProfiler.log
-      #contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
diff --git a/tests/modules/nf-core/fcs/fcsgx/main.nf b/tests/modules/nf-core/fcs/fcsgx/main.nf
deleted file mode 100644
index ff04a194dde0..000000000000
--- a/tests/modules/nf-core/fcs/fcsgx/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FCS_FCSGX } from '../../../../../modules/nf-core/fcs/fcsgx/main.nf'
-
-workflow test_fcs_fcsgx {
-
-    input = [
-        [ id:'test', taxid:'9606' ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
-    ]
-
-    database = [
-        file("https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxi"),
-        file("https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxs"),
-        file("https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.taxa.tsv"),
-        file("https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.meta.jsonl"),
-        file("https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.blast_div.tsv.gz")
-    ]
-    FCS_FCSGX ( input, database )
-}
diff --git a/tests/modules/nf-core/fcs/fcsgx/nextflow.config b/tests/modules/nf-core/fcs/fcsgx/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/fcs/fcsgx/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/fcs/fcsgx/test.yml b/tests/modules/nf-core/fcs/fcsgx/test.yml
deleted file mode 100644
index fe5a23e8eaf6..000000000000
--- a/tests/modules/nf-core/fcs/fcsgx/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: fcs fcsgx test_fcs_fcsgx
-  command: nextflow run ./tests/modules/nf-core/fcs/fcsgx -entry test_fcs_fcsgx -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fcs/fcsgx/nextflow.config
-  tags:
-    - fcs/fcsgx
-    - fcs
-  files:
-    - path: output/fcs/out/genome.fna.9606.fcs_gx_report.txt
-      contains: ["FCS genome report", "run-date", "prok:CFB group bacteria"]
-    - path: output/fcs/out/genome.fna.9606.taxonomy.rpt
-      contains: ["GX taxonomy analysis report", "run-date", "prok:CFB group bacteria"]
diff --git a/tests/modules/nf-core/gem2/gem2bedmappability/main.nf b/tests/modules/nf-core/gem2/gem2bedmappability/main.nf
deleted file mode 100644
index 7f0c7d854e72..000000000000
--- a/tests/modules/nf-core/gem2/gem2bedmappability/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GEM2_GEM2BEDMAPPABILITY   } from '../../../../../modules/nf-core/gem2/gem2bedmappability/main.nf'
-include { GEM2_GEMMAPPABILITY       } from '../../../../../modules/nf-core/gem2/gemmappability/main.nf'
-include { GEM2_GEMINDEXER           } from '../../../../../modules/nf-core/gem2/gemindexer/main.nf'
-
-workflow test_gem2_gem2bedmappability {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    GEM2_GEMINDEXER ( input )
-
-    GEM2_GEMMAPPABILITY ( GEM2_GEMINDEXER.out.index, "100" )
-
-    GEM2_GEM2BEDMAPPABILITY ( GEM2_GEMMAPPABILITY.out.map, GEM2_GEMINDEXER.out.index )
-}
diff --git a/tests/modules/nf-core/gem2/gem2bedmappability/nextflow.config b/tests/modules/nf-core/gem2/gem2bedmappability/nextflow.config
deleted file mode 100644
index 247772f85ccd..000000000000
--- a/tests/modules/nf-core/gem2/gem2bedmappability/nextflow.config
+++ /dev/null
@@ -1,12 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: GEM2_GEMINDEXER {
-        publishDir = [enabled:false]
-    }
-
-    withName: GEM2_GEMMAPPABILITY {
-        publishDir = [enabled:false]
-    }
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gem2/gem2bedmappability/test.yml b/tests/modules/nf-core/gem2/gem2bedmappability/test.yml
deleted file mode 100644
index 60271f4e2abf..000000000000
--- a/tests/modules/nf-core/gem2/gem2bedmappability/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: gem2 gem2bedmappability test_gem2_gem2bedmappability
-  command: nextflow run ./tests/modules/nf-core/gem2/gem2bedmappability -entry test_gem2_gem2bedmappability -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gem2/gem2bedmappability/nextflow.config
-  tags:
-    - gem2
-    - gem2/gem2bedmappability
-  files:
-    - path: output/gem2/test.bg
-      md5sum: 42596230d57c308892bcaefb3eabbf1b
-    - path: output/gem2/test.sizes
-      md5sum: 58102c0866e0bc69831c94d02fd859e1
-    - path: output/gem2/versions.yml
diff --git a/tests/modules/nf-core/gem2/gemmappability/main.nf b/tests/modules/nf-core/gem2/gemmappability/main.nf
deleted file mode 100644
index 21b403e86fe2..000000000000
--- a/tests/modules/nf-core/gem2/gemmappability/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GEM2_GEMMAPPABILITY } from '../../../../../modules/nf-core/gem2/gemmappability/main.nf'
-include { GEM2_GEMINDEXER     } from '../../../../../modules/nf-core/gem2/gemindexer/main.nf'
-
-workflow test_gem2_gemmappability {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    GEM2_GEMINDEXER ( input )
-
-    GEM2_GEMMAPPABILITY ( GEM2_GEMINDEXER.out.index, "100" )
-}
diff --git a/tests/modules/nf-core/gem2/gemmappability/nextflow.config b/tests/modules/nf-core/gem2/gemmappability/nextflow.config
deleted file mode 100644
index 35d34a63156b..000000000000
--- a/tests/modules/nf-core/gem2/gemmappability/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-    withName: GEM2_GEMINDEXER {
-        publishDir = [enabled:false]
-    }
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gem2/gemmappability/test.yml b/tests/modules/nf-core/gem2/gemmappability/test.yml
deleted file mode 100644
index bff542389836..000000000000
--- a/tests/modules/nf-core/gem2/gemmappability/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gem2 gemmappability test_gem2_gemmappability
-  command: nextflow run ./tests/modules/nf-core/gem2/gemmappability -entry test_gem2_gemmappability -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gem2/gemmappability/nextflow.config
-  tags:
-    - gem2
-    - gem2/gemmappability
-  files:
-    - path: output/gem2/test.mappability
-      md5sum: 8380b048fec0e8c4f104f49d2bf784c4
-    - path: output/gem2/versions.yml
diff --git a/tests/modules/nf-core/genescopefk/main.nf b/tests/modules/nf-core/genescopefk/main.nf
deleted file mode 100644
index fcd2fc491a5a..000000000000
--- a/tests/modules/nf-core/genescopefk/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK  } from '../../../../modules/nf-core/fastk/fastk/main.nf'
-include { FASTK_HISTEX } from '../../../../modules/nf-core/fastk/histex/main.nf'
-include { GENESCOPEFK  } from '../../../../modules/nf-core/genescopefk/main.nf'
-
-workflow test_genescopefk {
-
-    input = [
-        [ id:'test' , single_end: true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    FASTK_HISTEX ( FASTK_FASTK.out.hist )
-    GENESCOPEFK ( FASTK_HISTEX.out.hist )
-}
diff --git a/tests/modules/nf-core/genescopefk/nextflow.config b/tests/modules/nf-core/genescopefk/nextflow.config
deleted file mode 100644
index f01f56c7386a..000000000000
--- a/tests/modules/nf-core/genescopefk/nextflow.config
+++ /dev/null
@@ -1,15 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: 'FASTK_.*' {
-        publishDir = [ enabled: false ]
-    }
-    withName: 'FASTK_HISTEX' {
-        ext.args = '-G'
-    }
-    withName: 'GENESCOPEFK' {
-        ext.args = '--kmer_length 40 --ploidy 1'
-    }
-
-}
diff --git a/tests/modules/nf-core/genescopefk/test.yml b/tests/modules/nf-core/genescopefk/test.yml
deleted file mode 100644
index 4664582ff27e..000000000000
--- a/tests/modules/nf-core/genescopefk/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: genescopefk test_genescopefk
-  command: nextflow run ./tests/modules/nf-core/genescopefk -entry test_genescopefk -c ./tests/config/nextflow.config
-  tags:
-    - genescopefk
-  files:
-    - path: output/genescopefk/test_linear_plot.png
-      md5sum: bb221e2e21a6c0d04dcb6ec8f1bf1cd7
-    - path: output/genescopefk/test_log_plot.png
-      md5sum: d71ad0c963775992043c8f3c55d27fc4
-    - path: output/genescopefk/test_model.txt
-      md5sum: 49e5a66cf02b53a3b20880bfabef2ee8
-    - path: output/genescopefk/test_summary.txt
-      md5sum: 34540dcc2ba4ab9530f8878bbdc0921c
-    - path: output/genescopefk/test_transformed_linear_plot.png
-      md5sum: 3c8e3ad315e6c15cdf51c87de277ec1f
-    - path: output/genescopefk/test_transformed_log_plot.png
-      md5sum: 90d983c6faa9b8a02a1d26b777feefc6
-    - path: output/genescopefk/versions.yml
diff --git a/tests/modules/nf-core/genmap/map/main.nf b/tests/modules/nf-core/genmap/map/main.nf
deleted file mode 100644
index b2efe1f0cb68..000000000000
--- a/tests/modules/nf-core/genmap/map/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENMAP_INDEX  } from '../../../../../modules/nf-core/genmap/index/main.nf'
-include { GENMAP_MAP    } from '../../../../../modules/nf-core/genmap/map/main.nf'
-
-workflow test_genmap_map {
-
-    input = [
-        [id:"test"],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    beds = [
-        [id:"bed"],
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-
-    GENMAP_INDEX ( input )
-    GENMAP_MAP ( GENMAP_INDEX.out.index, beds )
-}
diff --git a/tests/modules/nf-core/genmap/map/nextflow.config b/tests/modules/nf-core/genmap/map/nextflow.config
deleted file mode 100644
index e55dfa1df8a0..000000000000
--- a/tests/modules/nf-core/genmap/map/nextflow.config
+++ /dev/null
@@ -1,14 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: GENMAP_INDEX {
-        publishDir = [enabled:false]
-    }
-
-    withName: GENMAP_MAP {
-        ext.prefix = "test_map"
-        ext.args = '-K 50 -E 2 -w -t -bg -d'
-    }
-
-}
diff --git a/tests/modules/nf-core/genmap/map/test.yml b/tests/modules/nf-core/genmap/map/test.yml
deleted file mode 100644
index 6be5197eb4c2..000000000000
--- a/tests/modules/nf-core/genmap/map/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: genmap map test_genmap_map
-  command: nextflow run ./tests/modules/nf-core/genmap/map -entry test_genmap_map -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmap/map/nextflow.config
-  tags:
-    - genmap/map
-    - genmap
-  files:
-    - path: output/genmap/test_map.bedgraph
-      md5sum: 27ca54c920f3ff0c5985384e557a40f2
-    - path: output/genmap/test_map.csv
-      md5sum: 4167a6c7ffbecc1a239c5c1e16b2cbc5
-    - path: output/genmap/test_map.txt
-      md5sum: 7f9aeaa3d174bb5e6f552efd4f857b4e
-    - path: output/genmap/test_map.wig
-      md5sum: c940a5c35af6ac1c11ecc87b7662fc2a
-    - path: output/genmap/versions.yml
diff --git a/tests/modules/nf-core/genotyphi/parse/main.nf b/tests/modules/nf-core/genotyphi/parse/main.nf
deleted file mode 100644
index 6e5f633ec1be..000000000000
--- a/tests/modules/nf-core/genotyphi/parse/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MYKROBE_PREDICT } from '../../../../../modules/nf-core/mykrobe/predict/main.nf'
-include { GENOTYPHI_PARSE } from '../../../../../modules/nf-core/genotyphi/parse/main.nf'
-
-workflow test_mykrobe_predict {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    MYKROBE_PREDICT ( input, "typhi" )
-    GENOTYPHI_PARSE ( MYKROBE_PREDICT.out.json )
-}
diff --git a/tests/modules/nf-core/genotyphi/parse/nextflow.config b/tests/modules/nf-core/genotyphi/parse/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/genotyphi/parse/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/genotyphi/parse/test.yml b/tests/modules/nf-core/genotyphi/parse/test.yml
deleted file mode 100644
index 925b9963d9c1..000000000000
--- a/tests/modules/nf-core/genotyphi/parse/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: genotyphi parse test_mykrobe_predict
-  command: nextflow run ./tests/modules/nf-core/genotyphi/parse -entry test_mykrobe_predict -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/genotyphi/parse/nextflow.config
-  tags:
-    - genotyphi/parse
-    - genotyphi
-  files:
-    - path: output/genotyphi/test_predictResults.tsv
-      contains: ["genome", "confidence", "supported", "test", "NA"]
-    - path: output/mykrobe/test.csv
-      contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
-    - path: output/mykrobe/test.json
-      contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]
diff --git a/tests/modules/nf-core/plink/indeppairwise/main.nf b/tests/modules/nf-core/plink/indeppairwise/main.nf
deleted file mode 100644
index 52f3fb395cef..000000000000
--- a/tests/modules/nf-core/plink/indeppairwise/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLINK_INDEPPAIRWISE } from '../../../../../modules/nf-core/plink/indeppairwise/main.nf'
-include { PLINK_VCF           } from '../../../../../modules/nf-core/plink/vcf/main.nf'
-
-workflow test_plink_indeppairwise {
-
-    input = [
-            [ id:'test', single_end:false ], // meta map
-            file("https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz", checkIfExists: true)
-            ]
-
-    PLINK_VCF ( input )
-
-    bed_ch = PLINK_VCF.out.bed
-    bim_ch = PLINK_VCF.out.bim
-    fam_ch = PLINK_VCF.out.fam
-
-    ch_bed_bim_fam = bed_ch.join(bim_ch).join(fam_ch)
-
-    ch_window_size = Channel.value(50)
-    ch_variant_count = Channel.value(5)
-    ch_r2_threshold = Channel.value(0.2)
-
-    PLINK_INDEPPAIRWISE ( ch_bed_bim_fam, ch_window_size, ch_variant_count, ch_r2_threshold )
-}
diff --git a/tests/modules/nf-core/plink/indeppairwise/nextflow.config b/tests/modules/nf-core/plink/indeppairwise/nextflow.config
deleted file mode 100644
index 973d82507e7e..000000000000
--- a/tests/modules/nf-core/plink/indeppairwise/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: PLINK_VCF {
-        ext.args = ' --make-bed --biallelic-only strict --vcf-half-call missing --allow-extra-chr'
-    }
-}
diff --git a/tests/modules/nf-core/plink/indeppairwise/test.yml b/tests/modules/nf-core/plink/indeppairwise/test.yml
deleted file mode 100644
index 20c6c0a5c788..000000000000
--- a/tests/modules/nf-core/plink/indeppairwise/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: plink indeppairwise test_plink_indeppairwise
-  command: nextflow run ./tests/modules/nf-core/plink/indeppairwise -entry test_plink_indeppairwise -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/plink/indeppairwise/nextflow.config
-  tags:
-    - plink
-    - plink/indeppairwise
-  files:
-    - path: output/plink/test.bed
-      md5sum: 0cbb7bb2e4c9e23c75da1f338f9268bf
-    - path: output/plink/test.bim
-      md5sum: fe302f9edc5a217e55f1b6b17f187d2e
-    - path: output/plink/test.fam
-      md5sum: 619946963dc461d0e2ae4359da08eeb2
-    - path: output/plink/test.prune.in
-      md5sum: 50c7ab703f7b5c01d7c7ddc7517aea37
-    - path: output/plink/test.prune.out
-      md5sum: 6104a59d98bda81014870ecd059573fb
-    - path: output/plink/versions.yml
diff --git a/tests/modules/nf-core/shigeifinder/main.nf b/tests/modules/nf-core/shigeifinder/main.nf
deleted file mode 100644
index d9d8f48444dc..000000000000
--- a/tests/modules/nf-core/shigeifinder/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SHIGEIFINDER } from '../../../../modules/nf-core/shigeifinder/main.nf'
-include { SHIGEIFINDER as SHIGEIFINDER_READS } from '../../../../modules/nf-core/shigeifinder/main.nf'
-
-workflow test_shigeifinder_assembly {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    SHIGEIFINDER ( input )
-}
-
-workflow test_shigeifinder_reads {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    SHIGEIFINDER_READS ( input )
-}
diff --git a/tests/modules/nf-core/shigeifinder/nextflow.config b/tests/modules/nf-core/shigeifinder/nextflow.config
deleted file mode 100644
index 05e45d893d88..000000000000
--- a/tests/modules/nf-core/shigeifinder/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: SHIGEIFINDER_READS {
-        ext.args = '-r '
-    }
-
-}
diff --git a/tests/modules/nf-core/shigeifinder/test.yml b/tests/modules/nf-core/shigeifinder/test.yml
deleted file mode 100644
index f42ab50904f3..000000000000
--- a/tests/modules/nf-core/shigeifinder/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: shigeifinder test_shigeifinder_assembly
-  command: nextflow run ./tests/modules/nf-core/shigeifinder -entry test_shigeifinder_assembly -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigeifinder/nextflow.config
-  tags:
-    - shigeifinder
-  files:
-    - path: output/shigeifinder/test.tsv
-      md5sum: b9b0837765b574c4c61e14d1e90179cc
-    - path: output/shigeifinder/versions.yml
-
-- name: shigeifinder test_shigeifinder_reads
-  command: nextflow run ./tests/modules/nf-core/shigeifinder -entry test_shigeifinder_reads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigeifinder/nextflow.config
-  tags:
-    - shigeifinder
-  files:
-    - path: output/shigeifinder/test.tsv
-      md5sum: 8f7f7db057d9c53abaa4c647532433ed
-    - path: output/shigeifinder/versions.yml
diff --git a/tests/modules/nf-core/stecfinder/main.nf b/tests/modules/nf-core/stecfinder/main.nf
deleted file mode 100644
index d27e21d8c302..000000000000
--- a/tests/modules/nf-core/stecfinder/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STECFINDER } from '../../../../modules/nf-core/stecfinder/main.nf'
-include { STECFINDER as STECFINDER_READS } from '../../../../modules/nf-core/stecfinder/main.nf'
-
-workflow test_stecfinder_fasta {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    STECFINDER ( input )
-}
-
-workflow test_stecfinder_reads {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
-    ]
-
-    STECFINDER_READS ( input )
-}
diff --git a/tests/modules/nf-core/stecfinder/nextflow.config b/tests/modules/nf-core/stecfinder/nextflow.config
deleted file mode 100644
index 73511a4546c9..000000000000
--- a/tests/modules/nf-core/stecfinder/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: STECFINDER_READS {
-        ext.args = '-r'
-    }
-
-}
diff --git a/tests/modules/nf-core/stecfinder/test.yml b/tests/modules/nf-core/stecfinder/test.yml
deleted file mode 100644
index 456bae89268c..000000000000
--- a/tests/modules/nf-core/stecfinder/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: stecfinder test_stecfinder_fasta
-  command: nextflow run ./tests/modules/nf-core/stecfinder -entry test_stecfinder_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stecfinder/nextflow.config
-  tags:
-    - stecfinder
-  files:
-    - path: output/stecfinder/test.tsv
-      md5sum: c17e1e69728b48c06c47a7d10086f1da
-    - path: output/stecfinder/versions.yml
-
-- name: stecfinder test_stecfinder_reads
-  command: nextflow run ./tests/modules/nf-core/stecfinder -entry test_stecfinder_reads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stecfinder/nextflow.config
-  tags:
-    - stecfinder
-  files:
-    - path: output/stecfinder/test.tsv
-      md5sum: f0a5c4e3509bc8bd03f09aa21c31c526
-    - path: output/stecfinder/versions.yml
diff --git a/tests/modules/nf-core/survivor/filter/main.nf b/tests/modules/nf-core/survivor/filter/main.nf
deleted file mode 100644
index 5a5d4314af53..000000000000
--- a/tests/modules/nf-core/survivor/filter/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SURVIVOR_FILTER  as SURVIVOR_FILTER_NO_BED} from '../../../../../modules/nf-core/survivor/filter/main.nf'
-include { SURVIVOR_FILTER  as SURVIVOR_FILTER_BED} from '../../../../../modules/nf-core/survivor/filter/main.nf'
-
-workflow test_survivor_filter_no_bed {
-    
-    input_no_bed = [
-        [ id:'test'], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-            []
-    ]
-
-    SURVIVOR_FILTER_NO_BED ( 
-        input_no_bed,
-        51,
-        10001,
-        0.01,
-        10
-    )
-
-}
-
-workflow test_survivor_filter {
-
-    input_bed = [
-        [ id:'test'], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-        ]
-
-    SURVIVOR_FILTER_BED ( 
-        input_bed,
-        51,
-        10001,
-        0.01,
-        10
-    )
-
-}
diff --git a/tests/modules/nf-core/survivor/filter/nextflow.config b/tests/modules/nf-core/survivor/filter/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/survivor/filter/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/survivor/filter/test.yml b/tests/modules/nf-core/survivor/filter/test.yml
deleted file mode 100644
index ebd79f201026..000000000000
--- a/tests/modules/nf-core/survivor/filter/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: "survivor filter without regions to ignore"
-  command: nextflow run ./tests/modules/nf-core/survivor/filter -entry test_survivor_filter_no_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/survivor/filter/nextflow.config
-  tags:
-    - survivor
-    - survivor/filter
-  files:
-    - path: output/survivor/test.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-      md5sum: ec23f83ba5bb098d45027e63fab93d05
-    - path: output/survivor/versions.yml
-      md5sum: 9dfd6d01fe01fbcee31c9a6da1c96f9f
-
-- name: "survivor filter with regions to ignore"
-  command: nextflow run ./tests/modules/nf-core/survivor/filter -entry test_survivor_filter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/survivor/filter/nextflow.config
-  tags:
-    - survivor
-    - survivor/filter
-  files:
-    - path: output/survivor/test.vcf
-      md5sum: ec23f83ba5bb098d45027e63fab93d05
-    - path: output/survivor/versions.yml
-      md5sum: 139b0674031a5ec44982107e7674de4f
diff --git a/tests/modules/nf-core/svtk/rdtest2vcf/main.nf b/tests/modules/nf-core/svtk/rdtest2vcf/main.nf
deleted file mode 100644
index be5c0a4972cf..000000000000
--- a/tests/modules/nf-core/svtk/rdtest2vcf/main.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SVTK_RDTEST2VCF } from '../../../../../modules/nf-core/svtk/rdtest2vcf/main.nf'
-include { SVTK_VCF2BED      } from '../../../../../modules/nf-core/svtk/vcf2bed/main.nf'
-include { MANTA_GERMLINE    } from '../../../../../modules/nf-core/manta/germline/main.nf'
-
-workflow test_svtk_rdtest2vcf {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        [],
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE (
-        input,
-        fasta,
-        fasta_fai
-    )
-
-    SVTK_VCF2BED (
-        MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by:0)
-    )
-
-    samples = Channel.of("test").collectFile(name: "samples.txt")
-
-    SVTK_RDTEST2VCF (
-        SVTK_VCF2BED.out.bed.combine(samples),
-        fasta_fai
-    )
-}
diff --git a/tests/modules/nf-core/svtk/rdtest2vcf/nextflow.config b/tests/modules/nf-core/svtk/rdtest2vcf/nextflow.config
deleted file mode 100644
index b155a95faa98..000000000000
--- a/tests/modules/nf-core/svtk/rdtest2vcf/nextflow.config
+++ /dev/null
@@ -1,17 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: MANTA_GERMLINE {
-        publishDir = [
-            enabled: false
-        ]
-    }
-
-    withName: SVTK_VCF2BED {
-        publishDir = [
-            enabled: false
-        ]
-    }
-
-}
diff --git a/tests/modules/nf-core/svtk/rdtest2vcf/test.yml b/tests/modules/nf-core/svtk/rdtest2vcf/test.yml
deleted file mode 100644
index ac952560b16f..000000000000
--- a/tests/modules/nf-core/svtk/rdtest2vcf/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: svtk rdtest2vcf test_svtk_rdtest2vcf
-  command: nextflow run ./tests/modules/nf-core/svtk/rdtest2vcf -entry test_svtk_rdtest2vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svtk/rdtest2vcf/nextflow.config
-  tags:
-    - svtk
-    - svtk/rdtest2vcf
-  files:
-    - path: output/svtk/test.vcf.gz
-      md5sum: e9aac8e86191597f3727252a3a5ccb78
-    - path: output/svtk/test.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
diff --git a/tests/modules/nf-core/svtk/standardize/main.nf b/tests/modules/nf-core/svtk/standardize/main.nf
deleted file mode 100644
index 0964ace06848..000000000000
--- a/tests/modules/nf-core/svtk/standardize/main.nf
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SVTK_STANDARDIZE } from '../../../../../modules/nf-core/svtk/standardize/main.nf'
-include { MANTA_GERMLINE   } from '../../../../../modules/nf-core/manta/germline/main.nf'
-
-workflow test_svtk_standardize {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE(
-        input,
-        fasta,
-        fasta_fai
-    )
-
-    SVTK_STANDARDIZE ( 
-        MANTA_GERMLINE.out.diploid_sv_vcf,
-        fasta_fai
-    )
-}
-
-workflow test_svtk_standardize_no_contigs {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE(
-        input,
-        fasta,
-        fasta_fai
-    )
-
-    SVTK_STANDARDIZE ( 
-        MANTA_GERMLINE.out.diploid_sv_vcf,
-        []
-    )
-}
diff --git a/tests/modules/nf-core/svtk/standardize/nextflow.config b/tests/modules/nf-core/svtk/standardize/nextflow.config
deleted file mode 100644
index f432a5e69bd9..000000000000
--- a/tests/modules/nf-core/svtk/standardize/nextflow.config
+++ /dev/null
@@ -1,12 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-    withName: SVTK_STANDARDIZE {
-        ext.args = [
-            args   : '',
-            caller : 'manta'
-        ]
-    }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/svtk/standardize/test.yml b/tests/modules/nf-core/svtk/standardize/test.yml
deleted file mode 100644
index cd0e9ea2ab79..000000000000
--- a/tests/modules/nf-core/svtk/standardize/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: svtk standardize test_svtk_standardize
-  command: nextflow run ./tests/modules/nf-core/svtk/standardize -entry test_svtk_standardize -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svtk/standardize/nextflow.config
-  tags:
-    - svtk
-    - svtk/standardize
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/svtk/test.std.vcf.gz
-      md5sum: f7530f3bc7e6020e758cc996adc8ae35
-
-- name: svtk standardize test_svtk_standardize_no_contigs
-  command: nextflow run ./tests/modules/nf-core/svtk/standardize -entry test_svtk_standardize_no_contigs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svtk/standardize/nextflow.config
-  tags:
-    - svtk
-    - svtk/standardize
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/svtk/test.std.vcf.gz
-      md5sum: ea67be7438a0fb72db8096e1bc1bb957
diff --git a/tests/modules/nf-core/ultra/index/main.nf b/tests/modules/nf-core/ultra/index/main.nf
new file mode 100644
index 000000000000..892f8d332e0c
--- /dev/null
+++ b/tests/modules/nf-core/ultra/index/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ULTRA_INDEX } from '../../../../../modules/nf-core/ultra/index/main.nf'
+include { GNU_SORT    } from '../../../../../modules/nf-core/gnu/sort/main.nf'
+
+workflow test_ultra_index {
+
+    input = [
+        [ id:'test' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
+    ]
+    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    GNU_SORT ( input )
+    ULTRA_INDEX ( genome, GNU_SORT.out.sorted.map{ it[1] } )
+}
diff --git a/tests/modules/nf-core/ultra/index/nextflow.config b/tests/modules/nf-core/ultra/index/nextflow.config
new file mode 100644
index 000000000000..bb62486aef24
--- /dev/null
+++ b/tests/modules/nf-core/ultra/index/nextflow.config
@@ -0,0 +1,14 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: GNU_SORT {
+        ext.args = '-k1,1 -k4,4n'
+        ext.prefix = { "${input.baseName}_sorted" }
+    }
+
+    withName: ULTRA_INDEX {
+        ext.args = '--disable_infer'
+    }
+
+}
diff --git a/tests/modules/nf-core/ultra/index/test.yml b/tests/modules/nf-core/ultra/index/test.yml
new file mode 100644
index 000000000000..85374f5851bb
--- /dev/null
+++ b/tests/modules/nf-core/ultra/index/test.yml
@@ -0,0 +1,31 @@
+- name: ultra index test_ultra_index
+  command: nextflow run ./tests/modules/nf-core/ultra/index -entry test_ultra_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ultra/index/nextflow.config
+  tags:
+    - ultra/index
+    - ultra
+  files:
+    - path: output/gnu/genome_sorted.gtf
+      md5sum: 5cc4a890e302e08c88c8645e62be50d6
+    - path: output/gnu/versions.yml
+    - path: output/ultra/all_splice_pairs_annotations.pickle
+    - path: output/ultra/all_splice_sites_annotations.pickle
+    - path: output/ultra/chr_to_id.pickle
+    - path: output/ultra/database.db
+    - path: output/ultra/exon_choordinates_to_id.pickle
+    - path: output/ultra/flank_choordinates.pickle
+    - path: output/ultra/gene_to_small_segments.pickle
+    - path: output/ultra/id_to_chr.pickle
+    - path: output/ultra/max_intron_chr.pickle
+    - path: output/ultra/parts_to_segments.pickle
+    - path: output/ultra/ref_exon_sequences.pickle
+    - path: output/ultra/ref_flank_sequences.pickle
+    - path: output/ultra/ref_part_sequences.pickle
+    - path: output/ultra/ref_segment_sequences.pickle
+    - path: output/ultra/refs_id_lengths.pickle
+    - path: output/ultra/refs_lengths.pickle
+    - path: output/ultra/segment_id_to_choordinates.pickle
+    - path: output/ultra/segment_to_gene.pickle
+    - path: output/ultra/segment_to_ref.pickle
+    - path: output/ultra/splices_to_transcripts.pickle
+    - path: output/ultra/transcripts_to_splices.pickle
+    - path: output/ultra/versions.yml
diff --git a/tests/modules/nf-core/vrhyme/extractunbinned/main.nf b/tests/modules/nf-core/vrhyme/extractunbinned/main.nf
deleted file mode 100644
index c30ee1b88213..000000000000
--- a/tests/modules/nf-core/vrhyme/extractunbinned/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP                    } from '../../../../../modules/nf-core/gunzip/main.nf'
-include { VRHYME_VRHYME             } from '../../../../../modules/nf-core/vrhyme/vrhyme/main.nf'
-include { VRHYME_EXTRACTUNBINNED    } from '../../../../../modules/nf-core/vrhyme/extractunbinned/main.nf'
-
-workflow test_vrhyme_extractunbinned {
-
-    reads = [
-        [ id:'test', single_end:false ], // meta map
-        [
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    fasta = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( fasta )
-
-    VRHYME_VRHYME ( reads , GUNZIP.out.gunzip )
-
-    VRHYME_EXTRACTUNBINNED ( VRHYME_VRHYME.out.membership , GUNZIP.out.gunzip )
-}
diff --git a/tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config b/tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/vrhyme/extractunbinned/test.yml b/tests/modules/nf-core/vrhyme/extractunbinned/test.yml
deleted file mode 100644
index 1c7dd18effae..000000000000
--- a/tests/modules/nf-core/vrhyme/extractunbinned/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: vrhyme extractunbinned test_vrhyme_extractunbinned
-  command: nextflow run ./tests/modules/nf-core/vrhyme/extractunbinned -entry test_vrhyme_extractunbinned -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config
-  tags:
-    - vrhyme
-    - vrhyme/extractunbinned
-  files:
-    - path: output/vrhyme/test_unbinned_sequences.fasta
-      md5sum: 816e986c8ad8f277eb4a4891a12d7aff
-    - path: output/vrhyme/versions.yml
-
-- name: vrhyme extractunbinned test_vrhyme_extractunbinned_stub
-  command: nextflow run ./tests/modules/nf-core/vrhyme/extractunbinned -entry test_vrhyme_extractunbinned -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config -stub-run
-  tags:
-    - vrhyme
-    - vrhyme/extractunbinned
-  files:
-    - path: output/vrhyme/test_unbinned_sequences.fasta
-    - path: output/vrhyme/versions.yml
diff --git a/tests/modules/nf-core/vrhyme/linkbins/main.nf b/tests/modules/nf-core/vrhyme/linkbins/main.nf
deleted file mode 100644
index c03ac4d6ebc0..000000000000
--- a/tests/modules/nf-core/vrhyme/linkbins/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP            } from '../../../../../modules/nf-core/gunzip/main.nf'
-include { VRHYME_VRHYME     } from '../../../../../modules/nf-core/vrhyme/vrhyme/main.nf'
-include { VRHYME_LINKBINS   } from '../../../../../modules/nf-core/vrhyme/linkbins/main.nf'
-
-workflow test_vrhyme_linkbins {
-
-    reads = [
-        [ id:'test', single_end:false ], // meta map
-        [
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    fasta = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( fasta )
-    VRHYME_VRHYME ( reads , GUNZIP.out.gunzip )
-    VRHYME_LINKBINS ( VRHYME_VRHYME.out.bins )
-}
diff --git a/tests/modules/nf-core/vrhyme/linkbins/nextflow.config b/tests/modules/nf-core/vrhyme/linkbins/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/vrhyme/linkbins/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/vrhyme/linkbins/test.yml b/tests/modules/nf-core/vrhyme/linkbins/test.yml
deleted file mode 100644
index f4b3bbb698c1..000000000000
--- a/tests/modules/nf-core/vrhyme/linkbins/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: vrhyme linkbins test_vrhyme_linkbins
-  command: nextflow run ./tests/modules/nf-core/vrhyme/linkbins -entry test_vrhyme_linkbins -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/linkbins/nextflow.config
-  tags:
-    - vrhyme/linkbins
-    - vrhyme
-  files:
-    - path: output/vrhyme/test_linked_bins.fasta
-      md5sum: 92cee5d85211d1e657f67ba75d3b2b30
-    - path: output/vrhyme/versions.yml
-
-- name: vrhyme linkbins test_vrhyme_linkbins_stub
-  command: nextflow run ./tests/modules/nf-core/vrhyme/linkbins -entry test_vrhyme_linkbins -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/linkbins/nextflow.config -stub-run
-  tags:
-    - vrhyme/linkbins
-    - vrhyme
-  files:
-    - path: output/vrhyme/test_linked_bins.fasta
-    - path: output/vrhyme/versions.yml