Sync template #63
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Sync template | |
| on: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| inputs: | |
| testpipeline: | |
| type: boolean | |
| description: Only run on nf-core/testpipeline? | |
| required: true | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| force_pr: | |
| description: "Force a PR to be created" | |
| type: boolean | |
| default: false | |
| pipeline: | |
| description: "Pipeline to sync" | |
| type: string | |
| default: "all" | |
| # 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 [ "${{ github.event.inputs.pipeline }}" != "all" ]; then | |
| curl -O https://nf-co.re/pipeline_names.json | |
| # check if the pipeline exists | |
| if ! grep -q "\"${{ 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 | |
| # use the github runner on release otherwise use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default | |
| runs-on: ${{github.event_name == 'release' && 'self-hosted' || github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| strategy: | |
| matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| name: Check out nf-core/tools | |
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| name: Check out nf-core/${{ 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@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| 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@v2 | |
| 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 pipelines 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: ${{ always() }} | |
| uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
| with: | |
| name: sync_log_${{ matrix.pipeline }} | |
| path: sync_log_${{ matrix.pipeline }}.txt |