tools/.github/workflows/sync.yml at 82141d5277dd3b89f98f58b7e552dd07d4360ac4 · nf-core/tools · GitHub

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name: Sync template
on:
  # release:
  #   types: [published]
  workflow_dispatch:
    inputs:
      testpipeline:
        type: boolean
        description: Only run on nf-core/testpipeline?
        required: true
      force_pr:
        description: "Force a PR to be created"
        type: boolean
        default: false
      pipeline:
        description: "Pipeline to sync"
        type: string
        default: "all"
      debug:
        description: "Enable debug/verbose mode (true or false)"
        type: boolean
        default: false
      blog_post:
        description: "link to release blogpost"
        type: string
        required: true

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  get-pipelines:
    runs-on: "ubuntu-latest"
    outputs:
      matrix: ${{ steps.set-matrix.outputs.matrix }}
    steps:
      - id: set-matrix
        run: |
          if [ "${{ github.event.inputs.testpipeline }}" == "true" ]; then
            echo '{"pipeline":["testpipeline"]}' > pipeline_names.json
          elif [ "${{ github.event.inputs.pipeline }}" != "all" ] && [ "${{ github.event.inputs.pipeline }}" != "" ]; then
            curl -O https://nf-co.re/pipeline_names.json
            # check if the pipeline exists
            if ! grep -q "\"${{ github.event.inputs.pipeline }}\"" pipeline_names.json; then
              echo "Pipeline ${{ github.event.inputs.pipeline }} does not exist"
              exit 1
            fi
            echo '{"pipeline":["${{ github.event.inputs.pipeline }}"]}' > pipeline_names.json
          else
            curl -O https://nf-co.re/pipeline_names.json
          fi
          echo "matrix=$(cat pipeline_names.json)" >> $GITHUB_OUTPUT

  sync:
    needs: get-pipelines
    runs-on:
      - runs-on=${{ github.run_id }}-sync
      - runner=4cpu-linux-x64
    strategy:
      matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
      fail-fast: false
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
        name: Check out nf-core/tools
        with:
          ref: ${{ github.ref_name }}

      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
        name: Check out nf-core/${{ matrix.pipeline }}
        with:
          repository: nf-core/${{ matrix.pipeline }}
          ref: dev
          token: ${{ secrets.nf_core_bot_auth_token }}
          path: nf-core/${{ matrix.pipeline }}
          fetch-depth: "0"

      - name: Set up Python 3.14
        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
        with:
          python-version: "3.14"

      - name: Install uv
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          enable-cache: true

      - name: Install python dependencies
        run: uv sync

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
        with:
          version: "latest-everything"

      - name: Set Git default branch from nextflow.config and set git default branch to that or "master"

        run: |
          pushd nf-core/${{ matrix.pipeline }}
          defaultBranch=$(grep -B5 -A5 "nextflowVersion" nextflow.config | grep "defaultBranch" | cut -d"=" -f2 | sed "s/'//g")
          if [ -z "$defaultBranch" ]; then
            defaultBranch="master"
          fi
          popd
          echo "Default branch: $defaultBranch"
          echo "defaultBranch=$defaultBranch" >> GITHUB_OUTPUT
          git config --global init.defaultBranch $defaultBranch

      - name: Run synchronisation
        if: github.repository == 'nf-core/tools'
        env:
          GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
        run: |
          git config --global user.email "core@nf-co.re"
          git config --global user.name "nf-core-bot"
          uv run nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
            ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }} \
            pipelines sync -d nf-core/${{ matrix.pipeline }} \
            --from-branch dev \
            --pull-request \
            --username nf-core-bot \
            --github-repository nf-core/${{ matrix.pipeline }} \
            --blog-post ${{inputs.blog_post}}

      - name: Upload sync log file artifact
        if: ${{ always() }}
        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
        with:
          name: sync_log_${{ matrix.pipeline }}
          path: sync_log_${{ matrix.pipeline }}.txt