Add --help-json flag for machine-readable CLI help
#13828
Workflow file for this run
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| name: Create a pipeline and run nf-core linting | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| MakeTestWorkflow: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-make-test-worfklow | |
| - runner=4cpu-linux-x64 | |
| env: | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "25.10.4" | |
| - "latest-everything" | |
| steps: | |
| - name: go to subdirectory and change nextflow workdir | |
| run: | | |
| mkdir -p create-lint-wf | |
| cd create-lint-wf | |
| export NXF_WORK=$(pwd) | |
| # Get the repo code | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| name: Check out source-code repository | |
| # Set up nf-core/tools | |
| - 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 --all-extras | |
| - 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: uv 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 's/TODO nf-core:/TODONT nf-core:/g' {} \; | |
| 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: uv run nf-core --log-file log.txt pipelines list | |
| working-directory: create-lint-wf | |
| - name: nf-core pipelines schema | |
| run: uv 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() |