v2.0.0: Refactor for sample-wise parameterisation

.github/CONTRIBUTING.md

@@ -78,7 +78,8 @@ 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. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 

.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"

.github/actions/nf-test/action.yml

@@ -0,0 +1,111 @@
+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_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/

.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/genomeassembler' && 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/genomeassembler' && 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/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: |

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.04.2"
+          - "24.10.5"
           - "latest-everything"
         ASSEMBLER:
           - "hifi_flye"

.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."

.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

.github/workflows/fix-linting.yml → .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

.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: |

.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 }}