Use new nf-test features #21
Workflow file for this run
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| name: Run Linting | |
| on: | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| 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_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| # FIXME Flip this off once we get to less than a couple hundred. Adding | |
| # this so it will only run against changed files. It'll make it much | |
| # easier to fix these as they come up rather than everything at once. | |
| with: | |
| extra_args: "" | |
| ################### | |
| # nf-core linting # | |
| ################### | |
| # TODO Move these to pre-commit | |
| # https://github.com/nf-core/tools/pull/3141 | |
| nf-core-changes: | |
| name: nf-core-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| tags: ${{ steps.filter.outputs.changes }} | |
| modules: ${{ steps.tags.outputs.modules }} | |
| subworkflows: ${{ steps.tags.outputs.subworkflows }} | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| token: "" | |
| - name: Fetch module tags | |
| id: tags | |
| run: | | |
| echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT | |
| echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT | |
| - name: debug | |
| run: | | |
| echo ${{ steps.tags.outputs.modules }} | |
| echo ${{ steps.tags.outputs.subworkflows }} | |
| nf-core-lint-modules: | |
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
| name: nf-core lint modules | |
| needs: nf-core-changes | |
| if: ${{ (needs.nf-core-changes.outputs.modules != '[]') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}" | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip | |
| restore-keys: | | |
| ${{ runner.os }}-pip | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint module ${{ matrix.tags }} | |
| run: nf-core modules lint ${{ matrix.tags }} | |
| nf-core-lint-subworkflows: | |
| runs-on: ubuntu-latest | |
| name: nf-core lint subworkflows | |
| needs: nf-core-changes | |
| if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}" | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint module ${{ matrix.tags }} | |
| run: nf-core subworkflows lint ${{ matrix.tags }} |