add more module to msa_structural_alignment #87
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| name: Run Linting | |
| on: | |
| pull_request: | |
| branches: [main] | |
| 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: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| with: | |
| extra_args: "" | |
| lint-changes: | |
| name: lint-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files | |
| subworkflows: ${{ steps.filter.outputs.subworkflows }} | |
| subworkflows_files: ${{ steps.subworkflow_names.outputs.result }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3 | |
| id: filter | |
| with: | |
| filters: | | |
| subworkflows: | |
| - added|modified: 'subworkflows/mirpedrol/**' | |
| token: "" | |
| list-files: "json" | |
| - name: Get subworkflow name | |
| uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7 | |
| id: subworkflow_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.subworkflows_files }} | |
| .map(path => path | |
| .replace('tests/', '') | |
| .replace('subworkflows/mirpedrol/', '') | |
| .split('/') | |
| .slice(0, 2) | |
| .filter(x => x !== 'main.nf' && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml' && !x.endsWith('.test') && !x.endsWith('.snap') && !x.endsWith('.config') && !x.endsWith('.diff')) | |
| .join('/')) | |
| ) | |
| ]; | |
| - name: debug | |
| run: | | |
| echo ${{ steps.filter.outputs.subworkflows_files }} | |
| echo ${{ steps.subworkflow_names.outputs.result }} | |
| lint-subworkflows: | |
| runs-on: ubuntu-latest | |
| name: lint-subworkflows | |
| needs: lint-changes | |
| if: ( needs.lint-changes.outputs.subworkflows_files != '[]') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.lint-changes.outputs.subworkflows_files) }}"] | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # 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: Install nf-class | |
| run: pip install git+https://github.com/mirpedrol/nf-class.git@dev | |
| - name: Lint subworkflow ${{ matrix.tags }} nf-core | |
| run: nf-core subworkflows lint ${{ matrix.tags }} | |
| continue-on-error: true | |
| - name: Lint subworkflow ${{ matrix.tags }} nf-class | |
| run: nf-class classes lint ${{ matrix.tags }} |