sync.yml

name: Sync template
on:
  release:
    types: [published]
  workflow_dispatch:
    inputs:
      testpipeline:
        type: boolean
        description: Only run on nf-core/testpipeline?
        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
          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: self-hosted
    strategy:
      matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
      fail-fast: false
    steps:
      - uses: actions/checkout@v4
        name: Check out nf-core/tools
        with:
          clean: false

      - uses: actions/checkout@v4
        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 3.12
        uses: actions/setup-python@v4
        with:
          python-version: 3.12

      - name: Install python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install .

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "latest-everything"

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

      - name: Upload sync log file artifact
        if: ${{ always() }}
        uses: actions/upload-artifact@v3
        with:
          name: sync_log_${{ matrix.pipeline }}
          path: sync_log_${{ matrix.pipeline }}.txt