From 67f6483260f2a9bc33ee593e3b04d3e11d8cec7e Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 30 Apr 2025 12:27:58 +0000
Subject: [PATCH 01/10] Template update for nf-core/tools version 3.2.1

---
 .github/workflows/awsfulltest.yml | 41 ++++++++-----------------------
 .github/workflows/ci.yml          |  1 +
 .nf-core.yml                      |  2 +-
 nextflow.config                   |  2 +-
 ro-crate-metadata.json            | 12 ++++-----
 5 files changed, 19 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index c44cd332a..5a98c9fde 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -4,44 +4,23 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
@@ -52,12 +31,12 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnaseq/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnaseq/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4a4e5fac6..2a764926c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -83,5 +83,6 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.nf-core.yml b/.nf-core.yml
index 97dadc8dd..65b7e4b50 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -11,7 +11,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
-nf_core_version: 3.2.0
+nf_core_version: 3.2.1
 repository_type: pipeline
 template:
   author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n"
diff --git a/nextflow.config b/nextflow.config
index 916d064b6..beaf97328 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -265,7 +265,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 2808958e8..d6d733a66 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-01-27T14:47:16+00:00",
+            "datePublished": "2025-04-30T12:27:54+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnaseq_logo_dark.png\">\n    <img alt=\"nf-core/rnaseq\" src=\"docs/images/nf-core-rnaseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnaseq** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/rnaseq \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnaseq/output).\n\n## Credits\n\nnf-core/rnaseq was originally written by Harshil Patel, Phil Ewels, Rickard Hammar\u00e9n.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#0bb8ad79-8c56-4c40-8c8f-3f3a759cb012"
+                    "@id": "#cd43f0fe-3ad6-4bc1-8cfb-75fa28b1a984"
                 }
             ],
             "name": "nf-core/rnaseq"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-01-27T14:47:16Z",
+            "dateModified": "2025-04-30T12:27:54Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "rna", "rna-seq"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#0bb8ad79-8c56-4c40-8c8f-3f3a759cb012",
+            "@id": "#cd43f0fe-3ad6-4bc1-8cfb-75fa28b1a984",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#23a449b9-016a-4957-a48a-d2dc5dc0b823"
+                    "@id": "#26d6a15d-107f-4ba0-b65e-85004e2a79f1"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/rnaseq"
         },
         {
-            "@id": "#23a449b9-016a-4957-a48a-d2dc5dc0b823",
+            "@id": "#26d6a15d-107f-4ba0-b65e-85004e2a79f1",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/rnaseq",
             "resource": "repos/nf-core/rnaseq/actions/workflows/ci.yml",

From 949f8fc0b210e424eba4f5f42cd63b8fa7efc311 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 3 Jun 2025 11:02:15 +0000
Subject: [PATCH 02/10] Template update for nf-core/tools version 3.3.1

---
 .editorconfig                                 |  37 -----
 .github/CONTRIBUTING.md                       |   2 +-
 .github/actions/get-shards/action.yml         |  69 +++++++++
 .github/actions/nf-test/action.yml            | 113 ++++++++++++++
 .github/workflows/awsfulltest.yml             |   4 +-
 .github/workflows/awstest.yml                 |   2 +-
 .github/workflows/ci.yml                      |  88 -----------
 .github/workflows/clean-up.yml                |   2 +-
 .github/workflows/download_pipeline.yml       |  20 +--
 .../{fix-linting.yml => fix_linting.yml}      |   4 +-
 .github/workflows/linting.yml                 |  15 +-
 .github/workflows/linting_comment.yml         |   4 +-
 .github/workflows/nf-test.yml                 | 142 ++++++++++++++++++
 .github/workflows/release-announcements.yml   |   2 +-
 ...mment.yml => template-version-comment.yml} |   2 +-
 .nf-core.yml                                  |   3 +-
 .pre-commit-config.yaml                       |  26 +++-
 .prettierrc.yml                               |   5 +
 README.md                                     |   7 +-
 conf/base.config                              |   5 +-
 nextflow.config                               |  17 ++-
 nf-test.config                                |  24 +++
 ro-crate-metadata.json                        |  16 +-
 .../utils_nfcore_rnaseq_pipeline/main.nf      |   1 -
 tests/.nftignore                              |  10 ++
 tests/default.nf.test                         |  35 +++++
 tests/nextflow.config                         |  12 ++
 27 files changed, 487 insertions(+), 180 deletions(-)
 delete mode 100644 .editorconfig
 create mode 100644 .github/actions/get-shards/action.yml
 create mode 100644 .github/actions/nf-test/action.yml
 delete mode 100644 .github/workflows/ci.yml
 rename .github/workflows/{fix-linting.yml => fix_linting.yml} (96%)
 create mode 100644 .github/workflows/nf-test.yml
 rename .github/workflows/{template_version_comment.yml => template-version-comment.yml} (95%)
 create mode 100644 nf-test.config
 create mode 100644 tests/.nftignore
 create mode 100644 tests/default.nf.test
 create mode 100644 tests/nextflow.config

diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 6d9b74cc0..000000000
--- a/.editorconfig
+++ /dev/null
@@ -1,37 +0,0 @@
-root = true
-
-[*]
-charset = utf-8
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true
-indent_size = 4
-indent_style = space
-
-[*.{md,yml,yaml,html,css,scss,js}]
-indent_size = 2
-
-# These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
-[/assets/email*]
-indent_size = unset
-
-# ignore python and markdown
-[*.{py,md}]
-indent_style = unset
-
-# ignore ro-crate metadata files
-[**/ro-crate-metadata.json]
-insert_final_newline = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 46fbf85c2..7abddde1d 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -78,7 +78,7 @@ If you wish to contribute a new step, please use the following coding standards:
 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+8. If applicable, add a new test in the `tests` directory.
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
new file mode 100644
index 000000000..34085279f
--- /dev/null
+++ b/.github/actions/get-shards/action.yml
@@ -0,0 +1,69 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+  max_shards:
+    description: "Maximum number of shards allowed"
+    required: true
+  paths:
+    description: "Component paths to test"
+    required: false
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+outputs:
+  shard:
+    description: "Array of shard numbers"
+    value: ${{ steps.shards.outputs.shard }}
+  total_shards:
+    description: "Total number of shards"
+    value: ${{ steps.shards.outputs.total_shards }}
+runs:
+  using: "composite"
+  steps:
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: ${{ env.NFT_VER }}
+    - name: Get number of shards
+      id: shards
+      shell: bash
+      run: |
+        # Run nf-test with dynamic parameter
+        nftest_output=$(nf-test test \
+          --profile +docker \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --dry-run \
+          --ci \
+          --changed-since HEAD^) || {
+            echo "nf-test command failed with exit code $?"
+            echo "Full output: $nftest_output"
+            exit 1
+        }
+        echo "nf-test dry-run output: $nftest_output"
+
+        # Default values for shard and total_shards
+        shard="[]"
+        total_shards=0
+
+        # Check if there are related tests
+        if echo "$nftest_output" | grep -q 'No tests to execute'; then
+          echo "No related tests found."
+        else
+          # Extract the number of related tests
+          number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
+          if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
+            shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
+            shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
+            total_shards="$shards_to_run"
+          else
+            echo "Unexpected output format. Falling back to default values."
+          fi
+        fi
+
+        # Write to GitHub Actions outputs
+        echo "shard=$shard" >> $GITHUB_OUTPUT
+        echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
+
+        # Debugging output
+        echo "Final shard array: $shard"
+        echo "Total number of shards: $total_shards"
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
new file mode 100644
index 000000000..243e78238
--- /dev/null
+++ b/.github/actions/nf-test/action.yml
@@ -0,0 +1,113 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+  profile:
+    description: "Profile to use"
+    required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  paths:
+    description: "Test paths"
+    required: true
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      with:
+        python-version: "3.13"
+
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "${{ env.NFT_VER }}"
+        install-pdiff: true
+
+    - name: Setup apptainer
+      if: contains(inputs.profile, 'singularity')
+      uses: eWaterCycle/setup-apptainer@main
+
+    - name: Set up Singularity
+      if: contains(inputs.profile, 'singularity')
+      shell: bash
+      run: |
+        mkdir -p $NXF_SINGULARITY_CACHEDIR
+        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+    - name: Conda setup
+      if: contains(inputs.profile, 'conda')
+      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      with:
+        auto-update-conda: true
+        conda-solver: libmamba
+        conda-remove-defaults: true
+
+      # TODO Skip failing conda tests and document their failures
+      # https://github.com/nf-core/modules/issues/7017
+    - name: Run nf-test
+      shell: bash
+      env:
+        NFT_DIFF: ${{ env.NFT_DIFF }}
+        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+        NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+      run: |
+        nf-test test \
+          --profile=+${{ inputs.profile }} \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --ci \
+          --changed-since HEAD^ \
+          --verbose \
+          --tap=test.tap \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
+
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+
+    - name: Generate test summary
+      if: always()
+      shell: bash
+      run: |
+        # Add header if it doesn't exist (using a token file to track this)
+        if [ ! -f ".summary_header" ]; then
+          echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+          touch .summary_header
+        fi
+
+        if [ -f test.tap ]; then
+          while IFS= read -r line; do
+            if [[ $line =~ ^ok ]]; then
+              test_name="${line#ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            elif [[ $line =~ ^not\ ok ]]; then
+              test_name="${line#not ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            fi
+          done < test.tap
+        else
+          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+        fi
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 5a98c9fde..c39baad00 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
   run-platform:
     name: Run AWS full tests
     # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
-    if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
+    if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
       - name: Set revision variable
@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 95bfa9ef4..f5c170fd7 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index 2a764926c..000000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,88 +0,0 @@
-name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on:
-  push:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
-  workflow_dispatch:
-
-env:
-  NXF_ANSI_LOG: false
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
-  cancel-in-progress: true
-
-jobs:
-  test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-        profile:
-          - "conda"
-          - "docker"
-          - "singularity"
-        test_name:
-          - "test"
-        isMaster:
-          - ${{ github.base_ref == 'master' }}
-        # Exclude conda and singularity on dev
-        exclude:
-          - isMaster: false
-            profile: "conda"
-          - isMaster: false
-            profile: "singularity"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          conda-solver: libmamba
-          channels: conda-forge,bioconda
-
-      - name: Set up Conda
-        if: matrix.profile == 'conda'
-        run: |
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
-        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 0b6b1f272..ac030fd58 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index ab06316ea..999bcc382 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -12,14 +12,6 @@ on:
         required: true
         default: "dev"
   pull_request:
-    types:
-      - opened
-      - edited
-      - synchronize
-    branches:
-      - main
-      - master
-  pull_request_target:
     branches:
       - main
       - master
@@ -52,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -120,6 +112,7 @@ jobs:
           echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
+        id: count_comparison
         run: |
           if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
             initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
@@ -132,3 +125,10 @@ jobs:
           else
             echo "The pipeline can be downloaded successfully!"
           fi
+
+      - name: Upload Nextflow logfile for debugging purposes
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: nextflow_logfile.txt
+          path: .nextflow.log*
+          include-hidden-files: true
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml
similarity index 96%
rename from .github/workflows/fix-linting.yml
rename to .github/workflows/fix_linting.yml
index b7a354b23..62a34d5ef 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5a2..f2d7d1dd7 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,9 +3,6 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -17,9 +14,9 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6af8..7e8050fb8 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
new file mode 100644
index 000000000..f03aea0c0
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,142 @@
+name: Run nf-test
+on:
+  push:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+jobs:
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: # use self-hosted runners
+      - runs-on=$-nf-test-changes
+      - runner=4cpu-linux-x64
+    outputs:
+      shard: ${{ steps.set-shards.outputs.shard }}
+      total_shards: ${{ steps.set-shards.outputs.total_shards }}
+    steps:
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: get number of shards
+        id: set-shards
+        uses: ./.github/actions/get-shards
+        env:
+          NFT_VER: ${{ env.NFT_VER }}
+        with:
+          max_shards: 7
+
+      - name: debug
+        run: |
+          echo ${{ steps.set-shards.outputs.shard }}
+          echo ${{ steps.set-shards.outputs.total_shards }}
+
+  nf-test:
+    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    runs-on: # use self-hosted runners
+      - runs-on=$-nf-test
+      - runner=4cpu-linux-x64
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [conda, docker, singularity]
+        isMain:
+          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMain: false
+            profile: "conda"
+          - isMain: false
+            profile: "singularity"
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: Run nf-test
+        uses: ./.github/actions/nf-test
+        env:
+          NFT_DIFF: ${{ env.NFT_DIFF }}
+          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+        with:
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+  confirm-pass:
+    needs: [nf-test]
+    if: always()
+    runs-on: # use self-hosted runners
+      - runs-on=$-confirm-pass
+      - runner=2cpu-linux-x64
+    steps:
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"
+
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        if: always()
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 76a9e67ed..4abaf4843 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
+      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml
similarity index 95%
rename from .github/workflows/template_version_comment.yml
rename to .github/workflows/template-version-comment.yml
index 537529bc1..beb5c77fb 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -14,7 +14,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: nichmor/minimal-read-yaml@v0.0.2
+        uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
diff --git a/.nf-core.yml b/.nf-core.yml
index 65b7e4b50..e72bad129 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,4 @@
 lint:
-  actions_ci: false
   files_exist:
     - conf/modules.config
   files_unchanged:
@@ -11,7 +10,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
-nf_core_version: 3.2.1
+nf_core_version: 3.3.1
 repository_type: pipeline
 template:
   author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1dec86502..9d0b248d3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,10 +4,24 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+          - prettier@3.5.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a766..07dbd8bb9 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2
diff --git a/README.md b/README.md
index 9efbb1044..e823a43aa 100644
--- a/README.md
+++ b/README.md
@@ -9,13 +9,14 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -28,7 +29,7 @@
 -->
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
+     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
diff --git a/conf/base.config b/conf/base.config
index 5d5c24d10..883f24d18 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,7 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
@@ -59,4 +59,7 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withLabel: process_gpu {
+        ext.use_gpu = { workflow.profile.contains('gpu') }
+    }
 }
diff --git a/nextflow.config b/nextflow.config
index beaf97328..283c9d48f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -160,16 +160,25 @@ profiles {
             ]
         }
     }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+    }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Load nf-core custom profiles from different Institutions
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+// Load nf-core custom profiles from different institutions
+
+// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
+// Load nf-core/rnaseq custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
 
 // Load nf-core/rnaseq custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null"
+// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -265,7 +274,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 000000000..889df7601
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,24 @@
+config {
+    // location for all nf-test tests
+    testsDir "."
+
+    // nf-test directory including temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "tests/nextflow.config"
+
+    // ignore tests coming from the nf-core/modules repo
+    ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+
+    // run all test with defined profile(s) from the main nextflow.config
+    profile "test"
+
+    // list of filenames or patterns that should be trigger a full test run
+    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+
+    // load the necessary plugins
+    plugins {
+        load "nft-utils@0.0.3"
+    }
+}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index d6d733a66..441a93005 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-04-30T12:27:54+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnaseq_logo_dark.png\">\n    <img alt=\"nf-core/rnaseq\" src=\"docs/images/nf-core-rnaseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnaseq** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/rnaseq \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnaseq/output).\n\n## Credits\n\nnf-core/rnaseq was originally written by Harshil Patel, Phil Ewels, Rickard Hammar\u00e9n.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-06-03T11:02:10+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnaseq_logo_dark.png\">\n    <img alt=\"nf-core/rnaseq\" src=\"docs/images/nf-core-rnaseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnaseq** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/rnaseq \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnaseq/output).\n\n## Credits\n\nnf-core/rnaseq was originally written by Harshil Patel, Phil Ewels, Rickard Hammar\u00e9n.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#cd43f0fe-3ad6-4bc1-8cfb-75fa28b1a984"
+                    "@id": "#75f4967a-2681-475e-96a0-5ce5bc0521b7"
                 }
             ],
             "name": "nf-core/rnaseq"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-04-30T12:27:54Z",
+            "dateModified": "2025-06-03T11:02:10Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "rna", "rna-seq"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#cd43f0fe-3ad6-4bc1-8cfb-75fa28b1a984",
+            "@id": "#75f4967a-2681-475e-96a0-5ce5bc0521b7",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#26d6a15d-107f-4ba0-b65e-85004e2a79f1"
+                    "@id": "#fa6744ce-944a-4de2-9c46-d4e1c31dba4b"
                 }
             ],
             "mainEntity": {
@@ -173,10 +173,10 @@
             "name": "Test suite for nf-core/rnaseq"
         },
         {
-            "@id": "#26d6a15d-107f-4ba0-b65e-85004e2a79f1",
+            "@id": "#fa6744ce-944a-4de2-9c46-d4e1c31dba4b",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/rnaseq",
-            "resource": "repos/nf-core/rnaseq/actions/workflows/ci.yml",
+            "resource": "repos/nf-core/rnaseq/actions/workflows/nf-test.yml",
             "runsOn": {
                 "@id": "https://w3id.org/ro/terms/test#GithubService"
             },
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
index 6fa1ce83e..569556ecb 100644
--- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
@@ -261,4 +261,3 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
-
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 000000000..c10bc1f11
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,10 @@
+.DS_Store
+multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/multiqc_report.html
+fastqc/*_fastqc.{html,zip}
+pipeline_info/*.{html,json,txt,yml}
diff --git a/tests/default.nf.test b/tests/default.nf.test
new file mode 100644
index 000000000..006143c31
--- /dev/null
+++ b/tests/default.nf.test
@@ -0,0 +1,35 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+
+    test("-profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 000000000..71c889879
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,12 @@
+/*
+========================================================================================
+    Nextflow config file for running nf-test tests
+========================================================================================
+*/
+
+// TODO nf-core: Specify any additional parameters here
+// Or any resources requirements
+params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnaseq'
+
+aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From ec14f2dbfd9f57679d641a00c1711f071190ca1e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 13:40:58 +0200
Subject: [PATCH 03/10] fix pipeline specific config

---
 nextflow.config | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index d47e9c342..0da93484b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -286,9 +286,8 @@ profiles {
 // Load nf-core/rnaseq custom profiles from different institutions.
 includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-
 // Load nf-core/rnaseq custom profiles from different institutions.
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null"
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled

From ba9afa225621cacf62764a233d3de48ccce00e18 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 13:42:26 +0200
Subject: [PATCH 04/10] fix whitespace

---
 tests/star_rsem.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test
index 864b0561f..33d05f50a 100644
--- a/tests/star_rsem.nf.test
+++ b/tests/star_rsem.nf.test
@@ -66,4 +66,3 @@ nextflow_pipeline {
         }
     }
 }
-

From 355041462fb738e3dbfa05e61d5d3a92489ceab8 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 14:04:01 +0200
Subject: [PATCH 05/10] fix linting

---
 modules/nf-core/fastqc/main.nf  | 22 ++++++++++-----------
 modules/nf-core/fastqc/meta.yml |  1 -
 ro-crate-metadata.json          | 34 +++++++++++++++++++++++++--------
 3 files changed, 37 insertions(+), 20 deletions(-)

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154a..d8989f481 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,5 +1,5 @@
 process FASTQC {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -19,30 +19,30 @@ process FASTQC {
     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}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to     = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
     // 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 = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
     """
-    printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
 
     fastqc \\
-        ${args} \\
-        --threads ${task.cpus} \\
-        --memory ${fastqc_memory} \\
-        ${renamed_files}
+        $args \\
+        --threads $task.cpus \\
+        --memory $fastqc_memory \\
+        $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 2b2e62b8a..4827da7af 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,7 +11,6 @@ tools:
         FastQC gives general quality metrics about your reads.
         It provides information about the quality score distribution
         across your reads, the per base sequence content (%A/C/G/T).
-
         You get information about adapter contamination and other
         overrepresented sequences.
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 441a93005..f5bac1122 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-06-03T11:02:10+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnaseq_logo_dark.png\">\n    <img alt=\"nf-core/rnaseq\" src=\"docs/images/nf-core-rnaseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnaseq** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/rnaseq \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnaseq/output).\n\n## Credits\n\nnf-core/rnaseq was originally written by Harshil Patel, Phil Ewels, Rickard Hammar\u00e9n.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnaseq_logo_dark.png\">\n    <img alt=\"nf-core/rnaseq\" src=\"docs/images/nf-core-rnaseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnaseq** is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report.\n\n![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey_animated.svg)\n\n> In case the image above is not loading, please have a look at the [static version](docs/images/nf-core-rnaseq_metro_map_grey.png).\n\n1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))\n2. Auto-infer strandedness by subsampling and pseudoalignment ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))\n3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n4. UMI extraction ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))\n5. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))\n6. Removal of genome contaminants ([`BBSplit`](http://seqanswers.com/forums/showthread.php?t=41288))\n7. Removal of ribosomal RNA ([`SortMeRNA`](https://github.com/biocore/sortmerna))\n8. Choice of multiple alignment and quantification routes:\n   1. [`STAR`](https://github.com/alexdobin/STAR) -> [`Salmon`](https://combine-lab.github.io/salmon/)\n   2. [`STAR`](https://github.com/alexdobin/STAR) -> [`RSEM`](https://github.com/deweylab/RSEM)\n   3. [`HiSAT2`](https://ccb.jhu.edu/software/hisat2/index.shtml) -> **NO QUANTIFICATION**\n9. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n10. UMI-based deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))\n11. Duplicate read marking ([`picard MarkDuplicates`](https://broadinstitute.github.io/picard/))\n12. Transcript assembly and quantification ([`StringTie`](https://ccb.jhu.edu/software/stringtie/))\n13. Create bigWig coverage files ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))\n14. Extensive quality control:\n    1. [`RSeQC`](http://rseqc.sourceforge.net/)\n    2. [`Qualimap`](http://qualimap.bioinfo.cipf.es/)\n    3. [`dupRadar`](https://bioconductor.org/packages/release/bioc/html/dupRadar.html)\n    4. [`Preseq`](http://smithlabresearch.org/software/preseq/)\n    5. [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)\n    6. [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) -> [`Bracken`](https://ccb.jhu.edu/software/bracken/) on unaligned sequences; _optional_\n15. Pseudoalignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_)\n16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))\n\n> **Note**\n> The SRA download functionality has been removed from the pipeline (`>=3.2`) and ported to an independent workflow called [nf-core/fetchngs](https://nf-co.re/fetchngs). You can provide `--nf_core_pipeline rnaseq` when running nf-core/fetchngs to download and auto-create a samplesheet containing publicly available samples that can be accepted directly as input by this pipeline.\n\n> **Warning**\n> Quantification isn't performed if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. However, you can use this route if you have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n**samplesheet.csv**:\n\n```csv\nsample,fastq_1,fastq_2,strandedness\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto\nCONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,auto\nCONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,auto\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically. The strandedness refers to the library preparation and will be automatically inferred if set to `auto`.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/rnaseq \\\n    --input <SAMPLESHEET> \\\n    --outdir <OUTDIR> \\\n    --gtf <GTF> \\\n    --fasta <GENOME FASTA> \\\n    -profile <docker/singularity/.../institute>\n```\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnaseq/output).\n\nThis pipeline quantifies RNA-sequenced reads relative to genes/transcripts in the genome and normalizes the resulting data. It does not compare the samples statistically in order to assign significance in the form of FDR or P-values. For downstream analyses, the output files from this pipeline can be analysed directly in statistical environments like [R](https://www.r-project.org/), [Julia](https://julialang.org/) or via the [nf-core/differentialabundance](https://github.com/nf-core/differentialabundance/) pipeline.\n\n## Online videos\n\nA short talk about the history, current status and functionality on offer in this pipeline was given by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) on [8th February 2022](https://nf-co.re/events/2022/bytesize-32-nf-core-rnaseq) as part of the nf-core/bytesize series.\n\nYou can find numerous talks on the [nf-core events page](https://nf-co.re/events) from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out!\n\n## Credits\n\nThese scripts were originally written for use at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammar\u00e9n ([@Hammarn](https://github.com/Hammarn)).\n\nThe pipeline was re-written in Nextflow DSL2 and is primarily maintained by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/).\n\nThe pipeline workflow diagram was initially designed by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)) and James Fellows Yates ([@jfy133](https://github.com/jfy133)), further modifications where made by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and Maxime Garcia ([@maxulysse](https://github.com/maxulysse)).\n\nMany thanks to other who have helped out along the way too, including (but not limited to):\n\n- [Alex Peltzer](https://github.com/apeltzer)\n- [Colin Davenport](https://github.com/colindaven)\n- [Denis Moreno](https://github.com/Galithil)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Gregor Sturm](https://github.com/grst)\n- [Jacki Buros Novik](https://github.com/jburos)\n- [Lorena Pantano](https://github.com/lpantano)\n- [Matthias Zepper](https://github.com/MatthiasZepper)\n- [Maxime Garcia](https://github.com/maxulysse)\n- [Olga Botvinnik](https://github.com/olgabot)\n- [@orzechoj](https://github.com/orzechoj)\n- [Paolo Di Tommaso](https://github.com/pditommaso)\n- [Rob Syme](https://github.com/robsyme)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1400710](https://doi.org/10.5281/zenodo.1400710)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -121,7 +121,11 @@
         },
         {
             "@id": "main.nf",
-            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
             "creator": [
                 {
                     "@id": "#phil.ewels@scilifelab.se"
@@ -130,22 +134,36 @@
             "dateCreated": "",
             "dateModified": "2025-06-03T11:02:10Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
-            "keywords": ["nf-core", "nextflow", "rna", "rna-seq"],
-            "license": ["MIT"],
+            "keywords": [
+                "nf-core",
+                "nextflow",
+                "rna",
+                "rna-seq"
+            ],
+            "license": [
+                "MIT"
+            ],
             "maintainer": [
                 {
                     "@id": "#phil.ewels@scilifelab.se"
                 }
             ],
-            "name": ["nf-core/rnaseq"],
+            "name": [
+                "nf-core/rnaseq"
+            ],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/rnaseq", "https://nf-co.re/rnaseq/dev/"],
-            "version": ["3.17.0dev"]
+            "url": [
+                "https://github.com/nf-core/rnaseq",
+                "https://nf-co.re/rnaseq/dev/"
+            ],
+            "version": [
+                "3.17.0dev"
+            ]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -308,4 +326,4 @@
             "name": "Phil Ewels"
         }
     ]
-}
+}
\ No newline at end of file

From 777c3d249172c9a8d798418fe6a8d2a69c8bd8f9 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 15:07:12 +0200
Subject: [PATCH 06/10] Update tests/nextflow.config

---
 tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index a23e64eec..2a56e60f2 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -7,7 +7,7 @@
 // TODO nf-core: Specify any additional parameters here
 // Or any resources requirements
 params.modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
-params.pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15'
+params.pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/'
 params.hisat2_build_memory          = '3.GB'
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From 1a6d9f206a6c801c1eea0a06107a3c270b4fcba6 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 17:32:59 +0200
Subject: [PATCH 07/10] setup pdiff

---
 .github/workflows/nf-test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index f03aea0c0..8a0bb298c 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -25,6 +25,8 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
   NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false

From 86f90e661e7a32907b837c9e9b11289a41f68597 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 17:46:48 +0200
Subject: [PATCH 08/10] Apply suggestions from code review

---
 tests/nextflow.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 2a56e60f2..0ce9735cd 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -9,6 +9,7 @@
 params.modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
 params.pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/'
 params.hisat2_build_memory          = '3.GB'
+outdir                              = 'results'
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
 

From 0bbdc4d121cf183b9b655f9265da9a96c3f2aaef Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 18:04:03 +0200
Subject: [PATCH 09/10] Update tests/nextflow.config

---
 tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 0ce9735cd..6ea8b2c71 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -9,7 +9,7 @@
 params.modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
 params.pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/'
 params.hisat2_build_memory          = '3.GB'
-outdir                              = 'results'
+params.outdir                       = 'results'
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
 

From 6afadbb77c406e290af623ce26b4d235ab45256a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 3 Jun 2025 18:38:53 +0200
Subject: [PATCH 10/10] update .nftignore and snapshots

---
 tests/.nftignore                            |  1 +
 tests/default.nf.test.snap                  |  5 -----
 tests/featurecounts_group_type.nf.test.snap |  5 -----
 tests/hisat2.nf.test.snap                   |  5 -----
 tests/min_mapped_reads.nf.test.snap         |  3 ---
 tests/remove_ribo_rna.nf.test.snap          |  5 -----
 tests/skip_trimming.nf.test.snap            |  5 -----
 tests/star_rsem.nf.test.snap                |  5 -----
 tests/umi.nf.test.snap                      | 10 ----------
 9 files changed, 1 insertion(+), 43 deletions(-)

diff --git a/tests/.nftignore b/tests/.nftignore
index 345a1c4f7..9b230b8be 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -18,6 +18,7 @@ umitools/*.umi_extract.log
 {hisat2,star_rsem,star_salmon}/*.{bam,bam.bai}
 {hisat2,star_rsem,star_salmon}/bigwig/*.{forward,reverse}.bigWig
 {hisat2,star_rsem,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf
+{hisat2,star_rsem,star_salmon}/dupradar/intercepts_slope/*_intercept_slope.txt
 {hisat2,star_rsem,star_salmon}/dupradar/histogram/*_expressionHist.pdf
 {hisat2,star_rsem,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf
 {hisat2,star_rsem,star_salmon}/featurecounts/*.featureCounts.txt.summary
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 3b6b6b481..6e102a654 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1419,11 +1419,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
                 "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0",
                 "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
-                "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898",
-                "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,2a5c8c10f4371048d7d459411b58b087",
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
index 7774b5eb1..869d56e1a 100644
--- a/tests/featurecounts_group_type.nf.test.snap
+++ b/tests/featurecounts_group_type.nf.test.snap
@@ -1384,11 +1384,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
                 "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0",
                 "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
-                "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898",
-                "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
                 "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
                 "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
                 "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
index ba6799920..b353a132f 100644
--- a/tests/hisat2.nf.test.snap
+++ b/tests/hisat2.nf.test.snap
@@ -1207,11 +1207,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,9a5c2672c5817e930c7b884ada8fd92c",
                 "WT_REP1_dupMatrix.txt:md5,11371da7a087879340c2e7e6842a5d89",
                 "WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,1285c70833b46849b726412858736ed7",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a2efe7c3cad6f910d5dc208c2825a245",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,117712525fcbd396f77710f4f4b605d9",
-                "WT_REP1_intercept_slope.txt:md5,df33cbc6c3cb1c85c0c06cdba7df3873",
-                "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,cd7494b3bb12295a287f36506638f3c6",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,a60088d7013eebeb240e02457431eedb",
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
index cd3703da2..627e34c21 100644
--- a/tests/min_mapped_reads.nf.test.snap
+++ b/tests/min_mapped_reads.nf.test.snap
@@ -1148,9 +1148,6 @@
                 "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217",
                 "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370",
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,2a5c8c10f4371048d7d459411b58b087",
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
index a661a42c3..9e63e545f 100644
--- a/tests/remove_ribo_rna.nf.test.snap
+++ b/tests/remove_ribo_rna.nf.test.snap
@@ -1335,11 +1335,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc",
                 "WT_REP1_dupMatrix.txt:md5,b82c4fed335d03e85c414c91c2efd461",
                 "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217",
-                "WT_REP1_intercept_slope.txt:md5,7db7a898152e8eaab96b1aaf0e567e50",
-                "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,accedae963f399d3b47effd8eda41edb",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,e37ededa12690a8ccae2eb42dac47ed6",
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index ddbe78bd4..ff5d9021e 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -1199,11 +1199,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,bf065e266566c3fb96dc9319a3ed12cf",
                 "WT_REP1_dupMatrix.txt:md5,04512c8be70c1898d0262935ed5ec5bd",
                 "WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,7962ee6ba989f9af6465aaf1101ba13b",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,6c69ccc819c14847eef319b7fa8ccb4f",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,147b051de3f1e5c75821176851d13612",
-                "WT_REP1_intercept_slope.txt:md5,395cde13da1a90cf4378be2597c4f297",
-                "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,bc80cee5887507179965623c3dfef4f9",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b1ed22e51a94a0ca8f030ff4e09295aa",
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
index 327a12726..cca45e1cd 100644
--- a/tests/star_rsem.nf.test.snap
+++ b/tests/star_rsem.nf.test.snap
@@ -1224,11 +1224,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa",
                 "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78",
                 "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,d280fe126a5e82d24121d8662fd5a161",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a498640b0f9e710311ebc3eb67cedbd0",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e",
-                "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965",
-                "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,5a7a4291e8ff6cc25a4eb72dfdf06b51",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,a8200ec76e7916dc1210447130f77bbf",
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
index c049fde43..1acd7c176 100644
--- a/tests/umi.nf.test.snap
+++ b/tests/umi.nf.test.snap
@@ -1397,11 +1397,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,ee34da4ee0f7b56c710f5df041f88f31",
                 "WT_REP1_dupMatrix.txt:md5,6416d48ec754942e0a5a0c1a81680fe5",
                 "WT_REP2_dupMatrix.txt:md5,60e583c84a0d8b31cb667703c56d6c33",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,6c1e7c494f765ff6466ab023d52a1d70",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,93a525d3bc1ebfeddc8f04f3c2238237",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,74f6210123d50c2001f20dad6283e856",
-                "WT_REP1_intercept_slope.txt:md5,4d428c55745bf9e2832d7fdb76b72088",
-                "WT_REP2_intercept_slope.txt:md5,d6a47171cb52331c5e6e21671152fb98",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,d0e2b4a2e14fa97ad49c4baacfb1d5e3",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,c90762d8ee1df9219dc643b68e464ca0",
@@ -2604,11 +2599,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,6726b1c5e63db1f6efd2882de701adc1",
                 "WT_REP1_dupMatrix.txt:md5,1d57d6942d0720bddd25ff260dce08fa",
                 "WT_REP2_dupMatrix.txt:md5,b944b0f71ef8a98b5a4d53f4542c8e6f",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,a07fbfcbd487003cdd2123cb89209d14",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,38cea811141edcfd28d1e7770628f6c9",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b897caec80a37ace72c156ed091acbcd",
-                "WT_REP1_intercept_slope.txt:md5,9895ef03e6f9282b11c4a32fe16a25b0",
-                "WT_REP2_intercept_slope.txt:md5,6c22669508aecfdfe5583c38496db314",
                 "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,8433a395e65315feb0f8bfca4a1d1aba",
                 "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
                 "RAP1_IAA_30M_REP1.featureCounts.txt:md5,1ecf699b693201b29cadd187bb0f2971",