CI #1
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| name: CI | |
| on: | |
| workflow_dispatch: | |
| concurrency: | |
| group: ci-${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| packages: read | |
| statuses: write | |
| jobs: | |
| format: | |
| name: Format workflow | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 15 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v5 | |
| with: | |
| fetch-depth: 0 | |
| persist-credentials: false | |
| - name: Format code base | |
| uses: super-linter/super-linter@v8.5.0 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_ALL_CODEBASE: true | |
| DEFAULT_BRANCH: main | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| VALIDATE_PYTHON_BLACK: true | |
| VALIDATE_YAML_PRETTIER: true | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Set up R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| packages: styler | |
| - name: Check R style | |
| run: Rscript -e 'changed <- styler::style_dir(".", dry = "on"); if (any(changed$changed)) quit(status = 1)' | |
| test: | |
| name: Test example data | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 45 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v5 | |
| with: | |
| persist-credentials: false | |
| - name: Restore test data and resources | |
| run: bash test/setup_test_resources.sh | |
| - name: Run workflow on example data | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| snakemake-version: 8.25.3 | |
| args: >- | |
| --cores all | |
| --sdm conda | |
| --conda-cleanup-pkgs cache | |
| --show-failed-logs | |
| show-disk-usage-on-error: true |