.github/workflows/test.yml #113
Workflow file for this run
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| name: Test | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| branches: | |
| - "**" | |
| jobs: | |
| skip_duplicate: | |
| permissions: | |
| actions: write | |
| contents: read | |
| runs-on: ubuntu-latest | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@v5.3.0 | |
| with: | |
| cancel_others: 'true' | |
| concurrent_skipping: 'same_content_newer' | |
| paths_ignore: '["**/README.md", "CITATION.cff"]' | |
| run_test_pipeline: | |
| needs: skip_duplicate | |
| if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channel-priority: strict | |
| activate-environment: snakemake | |
| auto-activate-base: false | |
| environment-file: .test/environment_7.32.4.yaml | |
| - name: Run test pipeline | |
| shell: bash -el {0} | |
| run: snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --use-conda -c1 --conda-frontend conda | |
| - name: Pack logs | |
| if: success() || failure() | |
| shell: bash -el {0} | |
| run: tar czf logs.tar.gz .test/output/logs .test/.snakemake/log | |
| - name: Upload output file | |
| if: success() || failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: output-logs | |
| path: logs.tar.gz |