Allow nf-core pipelines download -r to download commits
#7496
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| name: Create a pipeline and test it | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| RunTestWorkflow: | |
| # 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: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| env: | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| steps: | |
| - name: go to working directory | |
| run: | | |
| mkdir -p create-test-wf | |
| cd create-test-wf | |
| export NXF_WORK=$(pwd) | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| name: Check out source-code repository | |
| - 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: ${{ matrix.NXF_VER }} | |
| - name: Run nf-core/tools | |
| run: | | |
| mkdir create-test-wf && cd create-test-wf | |
| export NXF_WORK=$(pwd) | |
| nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" | |
| nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results | |
| - name: Upload log file artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 | |
| with: | |
| name: nf-core-log-file-${{ matrix.NXF_VER }} | |
| path: create-test-wf/log.txt | |
| - name: Cleanup work directory | |
| # cleanup work directory | |
| run: sudo rm -rf create-test-wf | |
| if: always() |