riasc is testing ScanNeo2 #361
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| name: Linting | |
| run-name: ${{ github.actor }} is testing ScanNeo2 | |
| on: [push] | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout with submodules | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 1 | |
| - name: Formatting | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - run: pwd | |
| - uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.tests' | |
| snakefile: 'workflow/Snakefile' | |
| args: '--lint --configfile .tests/integration/config_basic/config.yaml' | |
| #run-workflow: | |
| #runs-on: ubuntu-latest | |
| #needs: | |
| #- linting | |
| #- formatting | |
| #steps: | |
| #- name: Checkout repository with submodules | |
| #uses: actions/checkout@v3 | |
| #with: | |
| #submodules: recursive | |
| #- name: Test workflow (basic model, no batch_effects) | |
| #uses: snakemake/[email protected] | |
| #with: | |
| #directory: .test | |
| #snakefile: workflow/Snakefile | |
| #args: "--configfile .test/config_basic/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
| #- name: Test report (basic model, no batch_effects) | |
| #uses: snakemake/[email protected] | |
| #with: | |
| #directory: .test | |
| #snakefile: workflow/Snakefile | |
| #args: "--configfile .test/config_basic/config.yaml --report report.zip" | |
| #- name: Test workflow (multiple variables_of_interest, include batch_effects) | |
| #uses: snakemake/[email protected] | |
| #with: | |
| #directory: .test | |
| #snakefile: workflow/Snakefile | |
| #args: "--configfile .test/config_complex/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
| #- name: Test report (multiple variables_of_interest, include batch_effects) | |
| #uses: snakemake/[email protected] | |
| #with: | |
| #directory: .test | |
| #snakefile: workflow/Snakefile | |
| #args: "--configfile .test/config_complex/config.yaml --report report.zip"b |