Update and nf-test sentieon/tnscope and sentieon/tnhaplotyper2

.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"
@@ -30,22 +30,14 @@ 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
       with:
         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

.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": [

.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:

.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()

.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"

.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 "[email protected]"
+          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

.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

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

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)

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"
     }
 }

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

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)