Fix GitHub action dependency error #103
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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/[email protected] | |
| 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 mamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| auto-activate-base: true | |
| activate-environment: "" | |
| - name: Install Snakemake 7.32 | |
| run: | | |
| pip install snakemake==7.32.4 | |
| - name: Run test pipeline | |
| run: | | |
| snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --use-conda -c1 | |
| - name: Pack logs | |
| shell: bash | |
| run: | | |
| tar czf logs.tar.gz .test/output/logs | |
| - name: Upload output file | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: output-logs | |
| path: logs.tar.gz |