Sync template #105
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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 | |
| 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" | |
| debug: | |
| description: "Enable debug/verbose mode (true or false)" | |
| type: boolean | |
| default: false | |
| # 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 | |
| # 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: ${{fromJson(needs.get-pipelines.outputs.matrix)}} | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| name: Check out nf-core/tools | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| name: Check out nf-core/${{ 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@0b93645e9fea7318ecaed2b359559ac225c90a2b # 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: 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) | |
| 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: ${{ secrets.nf_core_bot_auth_token }} | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "nf-core-bot" | |
| setBranch=$(git config --global init.defaultBranch) | |
| echo "set default branch: $setBranch" | |
| nf-core --log-file sync_log_${{ 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 }} | |
| - name: Upload sync log file artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 | |
| with: | |
| name: sync_log_${{ matrix.pipeline }} | |
| path: sync_log_${{ matrix.pipeline }}.txt |