Fix workflow links and update wrapper prefix #51
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Lint workflow | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| stagein: micromamba install -y -c conda-forge -c anaconda rsync conda | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: Linting | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| - name: Test workflow (local test data) | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--use-conda --show-failed-logs -j 10 --retries 1 --rerun-incomplete --keep-going --conda-cleanup-pkgs cache --wrapper-prefix file:///github/workspace/workflow/wrappers" | |
| stagein: micromamba install -y -c conda-forge -c anaconda rsync conda | |
| - name: Test report | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--report report.zip --wrapper-prefix file:///github/workspace/workflow/wrappers" | |
| stagein: micromamba install -y -c conda-forge -c anaconda rsync conda |