MosaiCatcher basic checks #498
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| name: MosaiCatcher basic checks | |
| on: | |
| schedule: | |
| # Run every Sunday at 00:00 UTC on the master branch | |
| - cron: "0 0 * * 0" | |
| # branches: | |
| # - master | |
| push: | |
| branches: | |
| - "*" | |
| - "!master" | |
| jobs: | |
| # WORK | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3.2.0 | |
| - name: Formatting | |
| uses: github/super-linter@v4 | |
| 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@v3.2.0 | |
| - name: Linting | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: ./workflow/Snakefile | |
| args: "--lint" | |
| Testing: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Linting | |
| # - Formatting | |
| steps: | |
| - uses: actions/checkout@v3.2.0 | |
| - name: Testing data | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: ./workflow/Snakefile | |
| stagein: "conda config --set channel_priority flexible" | |
| args: "--cores 1 --use-conda --latency-wait 60 --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug" | |
| - name: Testing report | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: ./workflow/Snakefile | |
| args: "--cores 1 --use-conda --latency-wait 60 --configfile .tests/config/simple_config.yaml --conda-frontend mamba --report report.zip" |