Relaxed regex for sample naming #16
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| name: CI | |
| on: | |
| push: | |
| branches: [master, main] | |
| pull_request: | |
| branches: [master, main] | |
| workflow_dispatch: | |
| jobs: | |
| Unit_testing: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest | |
| if [ -f .tests/unit/requirements.txt ]; then pip install -r .tests/unit/requirements.txt; fi | |
| - name: Unit testing | |
| run: | | |
| pytest .tests/unit | |
| - name: Cancelling parallel jobs | |
| if: failure() | |
| uses: andymckay/[email protected] | |
| Integration_testing: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Integration testing | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: '.tests/integration' | |
| snakefile: 'workflow/Snakefile' | |
| args: "--cores 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/integration/config/config.yaml" | |
| stagein: | | |
| conda config --set channel_priority strict | |
| - name: Archive logs on fail | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: fail-logs | |
| path: | | |
| .tests/integration/logs/ | |
| if-no-files-found: warn | |
| retention-days: 3 |