Use log warning to show empty VCF #336
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| name: Install | |
| on: [push, pull_request] | |
| 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' | |
| Install: | |
| 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' 'pulp<2.8' | |
| - name: Create environments | |
| run: | | |
| snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --conda-create-envs-only --use-conda -c1 | |
| Dry_run: | |
| 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' 'pulp<2.8' | |
| - name: Dry run | |
| run: | | |
| snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --dry-run |