Use updated pipeline commands in docstrings #9101
Workflow file for this run
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| name: Create a pipeline and run nf-core linting | |
| 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 | |
| env: | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| MakeTestWorkflow: | |
| runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| env: | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| steps: | |
| - name: go to subdirectory and change nextflow workdir | |
| run: | | |
| mkdir -p create-lint-wf | |
| cd create-lint-wf | |
| export NXF_WORK=$(pwd) | |
| # Get the repo code | |
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| name: Check out source-code repository | |
| # Set up nf-core/tools | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| with: | |
| python-version: "3.12" | |
| cache: pip | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: run create-lint-wf | |
| uses: ./.github/actions/create-lint-wf | |
| with: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| # Build a module from the template | |
| - name: nf-core modules create | |
| run: nf-core --verbose --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta | |
| working-directory: create-lint-wf | |
| # Remove TODO statements | |
| - name: remove TODO | |
| run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; | |
| working-directory: create-lint-wf | |
| # Uncomment includeConfig statement | |
| - name: uncomment include config | |
| run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; | |
| working-directory: create-lint-wf | |
| # Run the other nf-core commands | |
| - name: nf-core pipelines list | |
| run: nf-core --log-file log.txt pipelines list | |
| working-directory: create-lint-wf | |
| - name: nf-core pipelines schema | |
| run: nf-core --log-file log.txt pipelines schema build --dir nf-core-testpipeline/ --no-prompts | |
| working-directory: create-lint-wf | |
| - name: Cleanup work directory | |
| run: sudo rm -rf create-lint-wf | |
| if: always() |