Use new nf-test features #12
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: "" | ||
| prettier: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Check out repository | ||
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
| - name: Install NodeJS | ||
| uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 | ||
| with: | ||
| node-version: "20" | ||
| - name: Install Prettier | ||
| run: npm install -g [email protected] | ||
| - name: Run Prettier --check | ||
| run: prettier --check . | ||
| editorconfig: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
| - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 | ||
| with: | ||
| node-version: "20" | ||
| - name: Install editorconfig-checker | ||
| run: npm install -g editorconfig-checker | ||
| - name: Run ECLint check | ||
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | ||
| ################### | ||
| # nf-core linting # | ||
| ################### | ||
| 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: | ||
|
Check failure on line 106 in .github/workflows/lint.yml
|
||
| 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@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # 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-modules | ||
| 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@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # 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 }} | ||
