lint-pipelines.yml

name: Lint nf-core Pipelines

on:
  schedule:
    # Run nightly at midnight UTC
    - cron: "0 0 * * *"
  workflow_dispatch:
    inputs:
      pipelines:
        description: "Specific pipeline(s) to lint (comma-separated, leave empty for all)"
        type: string
        default: ""
      modules:
        description: "Specific module(s) to lint (comma-separated, leave empty for all)"
        type: string
        default: ""
      subworkflows:
        description: "Specific subworkflow(s) to lint (comma-separated, leave empty for all)"
        type: string
        default: ""
      skip_pipelines:
        description: "Skip linting pipelines"
        type: boolean
        default: false
      skip_modules:
        description: "Skip linting modules"
        type: boolean
        default: false
      skip_subworkflows:
        description: "Skip linting subworkflows"
        type: boolean
        default: false
      no_cache:
        description: "Skip linting cache to force fresh linting of all files"
        type: boolean
        default: false

permissions:
  contents: write

jobs:
  # Setup job: Get Nextflow commit SHA for caching
  setup:
    runs-on: ubuntu-latest
    outputs:
      nf-commit: ${{ steps.nf-commit.outputs.sha }}
    steps:
      - name: Get Nextflow latest commit
        id: nf-commit
        run: |
          COMMIT=$(git ls-remote https://github.com/nextflow-io/nextflow.git HEAD | cut -f1)
          echo "sha=$COMMIT" >> $GITHUB_OUTPUT

  # Build Nextflow and upload as artifact
  build-nextflow:
    runs-on: ubuntu-latest
    needs: setup
    steps:
      - name: Restore Nextflow build cache
        id: cache-nextflow
        uses: actions/cache/restore@v4
        with:
          path: nextflow-src/build/releases
          key: nextflow-build-${{ needs.setup.outputs.nf-commit }}

      - name: Set up Java
        if: steps.cache-nextflow.outputs.cache-hit != 'true'
        uses: actions/setup-java@v4
        with:
          distribution: "temurin"
          java-version: "21"

      - name: Clone and build Nextflow
        id: build-nextflow
        if: steps.cache-nextflow.outputs.cache-hit != 'true'
        run: |
          git clone --depth 1 https://github.com/nextflow-io/nextflow.git nextflow-src
          cd nextflow-src
          make pack
          cd build/releases/
          ln -s nextflow-*-dist nextflow

      - name: Save Nextflow build cache
        if: steps.cache-nextflow.outputs.cache-hit != 'true' && steps.build-nextflow.outcome == 'success'
        uses: actions/cache/save@v4
        with:
          path: nextflow-src/build/releases
          key: nextflow-build-${{ needs.setup.outputs.nf-commit }}

      - name: Fix symlink if needed
        run: |
          cd nextflow-src/build/releases
          if [ -L nextflow ] && [ ! -e nextflow ]; then
            rm nextflow
            ln -s nextflow-*-dist nextflow
          fi

      - name: Upload Nextflow binary
        uses: actions/upload-artifact@v4
        with:
          name: nextflow-binary
          path: nextflow-src/build/releases/
          retention-days: 1

  lint:
    runs-on: ubuntu-latest
    needs: [setup, build-nextflow]
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"

      - name: Download Nextflow binary
        uses: actions/download-artifact@v4
        with:
          name: nextflow-binary
          path: nextflow-src/build/releases

      - name: Add Nextflow to PATH
        run: |
          chmod +x nextflow-src/build/releases/nextflow*
          # Fix symlink if needed
          cd nextflow-src/build/releases
          if [ -L nextflow ] && [ ! -e nextflow ]; then
            rm nextflow
            ln -s nextflow-*-dist nextflow
          fi
          echo "${{ github.workspace }}/nextflow-src/build/releases" >> $GITHUB_PATH

      - name: Install dependencies
        run: pip install .

      - name: Build linting command
        id: build-cmd
        run: |
          CMD="strict-syntax-health --update-pipelines --update-readme"

          # Add skip flags based on inputs
          if [[ "${{ inputs.skip_pipelines }}" == "true" ]]; then
            CMD="$CMD --skip-pipelines"
          fi
          if [[ "${{ inputs.skip_modules }}" == "true" ]]; then
            CMD="$CMD --skip-modules"
          fi
          if [[ "${{ inputs.skip_subworkflows }}" == "true" ]]; then
            CMD="$CMD --skip-subworkflows"
          fi
          if [[ "${{ inputs.no_cache }}" == "true" ]]; then
            CMD="$CMD --no-cache"
          fi

          # Add specific filters if provided
          if [[ -n "${{ inputs.pipelines }}" ]]; then
            IFS=',' read -ra ITEMS <<< "${{ inputs.pipelines }}"
            for item in "${ITEMS[@]}"; do
              item=$(echo "$item" | xargs)
              [[ -n "$item" ]] && CMD="$CMD -p $item"
            done
          fi

          if [[ -n "${{ inputs.modules }}" ]]; then
            IFS=',' read -ra ITEMS <<< "${{ inputs.modules }}"
            for item in "${ITEMS[@]}"; do
              item=$(echo "$item" | xargs)
              [[ -n "$item" ]] && CMD="$CMD -m $item"
            done
          fi

          if [[ -n "${{ inputs.subworkflows }}" ]]; then
            IFS=',' read -ra ITEMS <<< "${{ inputs.subworkflows }}"
            for item in "${ITEMS[@]}"; do
              item=$(echo "$item" | xargs)
              [[ -n "$item" ]] && CMD="$CMD -s $item"
            done
          fi

          echo "cmd=$CMD" >> $GITHUB_OUTPUT
          echo "Running: $CMD"

      - name: Run linting
        run: ${{ steps.build-cmd.outputs.cmd }}

      - name: Run prek on all files to fix formatting
        uses: j178/prek-action@v1
        with:
          install-only: true
      - run: prek run --all-files || true

      - name: Commit and push changes
        run: |
          git config --local user.email "github-actions[bot]@users.noreply.github.com"
          git config --local user.name "github-actions[bot]"
          git add README.md lint_results/
          git diff --staged --quiet || git commit -m "Update lint results [skip ci]"
          git push