Fix GitHub action dependency error #103
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 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 |