Merge pull request #51 from nf-core/nf-core-template-merge-3.3.1

Important! Template update for nf-core/tools v3.3.1

Author: olgabot

.editorconfig

@@ -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`.
 

.github/CONTRIBUTING.md

@@ -7,6 +7,9 @@ inputs:
   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"
@@ -27,9 +30,9 @@ runs:
       run: |
         # Run nf-test with dynamic parameter
         nftest_output=$(nf-test test \
-          --dry-run \
           --profile +docker \
-          --filter function,workflow,pipeline \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --dry-run \
           --ci \
           --changed-since HEAD^) || {
             echo "nf-test command failed with exit code $?"

.github/actions/get-shards/action.yml

@@ -13,7 +13,9 @@ inputs:
   paths:
     description: "Test paths"
     required: true
-
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
 runs:
   using: "composite"
   steps:
@@ -23,14 +25,15 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
+      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
       with:
-        python-version: "3.11"
+        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')
@@ -44,21 +47,12 @@ runs:
         mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
     - name: Conda setup
-      if: ${{inputs.profile == 'conda'}}
+      if: contains(inputs.profile, 'conda')
       uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
       with:
         auto-update-conda: true
         conda-solver: libmamba
         conda-remove-defaults: true
-
-    - name: Install pdiff
-      shell: bash
-      run: |
-        python -m pip install pdiff
-
-    - name: Clean up Disk space
-      uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
@@ -70,12 +64,12 @@ runs:
       run: |
         nf-test test \
           --profile=+${{ inputs.profile }} \
-          --tap=test.tap \
-          --verbose \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
           --ci \
           --changed-since HEAD^ \
-          --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
-          --filter function,workflow,pipeline
+          --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

.github/actions/nf-test/action.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/proteinannotator' && 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/proteinannotator' && 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: |

.github/workflows/awsfulltest.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: |

.github/workflows/awstest.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."

.github/workflows/clean-up.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

.github/workflows/download_pipeline.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

.github/workflows/fix-linting.yml .github/workflows/fix_linting.yml.github/workflows/fix-linting.yml renamed to .github/workflows/fix_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: |