Sync template #196
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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 |