Update to snakemake8 #44
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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 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| 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: Unpack test data | |
| run: | | |
| mkdir -p .tests/integration/data/Listeria_cgmlst_Ruppitsch_chewbbaca | |
| tar -xzf .tests/integration/data/Ruppitsch_chewbbacca.tar.gz -C .tests/integration/data/Listeria_cgmlst_Ruppitsch_chewbbaca --strip-components 1 | |
| - name: Setup mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| activate-environment: snkmk | |
| - name: Integration testing | |
| run: | | |
| mamba install 'snakemake>=6.3.0' -n snkmk | |
| mamba env export | |
| /usr/share/miniconda3/envs/snkmk/bin/snakemake -s workflow/Snakefile --cores 1 --software-deployment-method conda --conda-prefix envs --show-failed-logs --configfile .tests/integration/config/config.yaml --keep-incomplete | |
| - name: Archive logs on fail | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: fail-logs | |
| path: | | |
| .tests/integration/logs/ | |
| .tests/integration/allele_calling/logs | |
| .tests/integration/join_clusters_main/logs | |
| .tests/integration/join_clusters_sub/logs | |
| if-no-files-found: warn | |
| retention-days: 3 |