filter bams for pp mapped reads for seacr #1071
Workflow file for this run
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| name: Python package | |
| on: [push] | |
| jobs: | |
| Test: | |
| if: github.event_name == 'pull_request' || github.event_name == 'push' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| test: ["config", "design", "pipeline"] | |
| assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Cache dependencies | |
| id: cache-env | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.conda | |
| ~/.cache/pip | |
| key: ${{ runner.os }}-env-${{ hashFiles('**/testing.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-env- | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: testing.yml | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| use-mamba: true | |
| - name: Install package | |
| shell: pwsh | |
| run: | | |
| pip install . | |
| - name: Cache singularity | |
| if: matrix.test == 'pipeline' | |
| id: cache-singularity | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.apptainer | |
| key: ${{ runner.os }}-singularity-${{ hashFiles('tmp/*') }} | |
| restore-keys: | | |
| ${{ runner.os }}-singularity- | |
| - uses: eWaterCycle/setup-apptainer@v2 | |
| if: matrix.test == 'pipeline' | |
| with: | |
| apptainer-version: 1.1.2 | |
| - name: Add singularity hub remote | |
| if: matrix.test == 'pipeline' | |
| shell: pwsh | |
| run: | | |
| apptainer remote add --no-login SylabsCloud cloud.sylabs.io | |
| apptainer remote use SylabsCloud | |
| - name: Pull singularity images | |
| if: matrix.test == 'pipeline' && steps.cache-singularity.outputs.cache-hit != 'true' | |
| shell: bash | |
| run: | | |
| echo "Pulling singularity images from the remote repository..." | |
| mkdir -p tmp | |
| if [[ "${{ matrix.test }}" == "pipeline" ]]; then | |
| apptainer pull --force library://asmith151/seqnado/seqnado_pipeline:latest | |
| elif [[ "${{ matrix.assay }}" == "atac" || "${{ matrix.assay }}" == "chip" ]]; then | |
| apptainer pull --force library://asmith151/seqnado/seqnado_extra:latest | |
| elif [[ "${{ matrix.assay }}" == "rna-rx" ]]; then | |
| apptainer pull --force library://asmith151/seqnado/seqnado_report:latest | |
| fi | |
| - name: Test ${{ matrix.test }} ${{ matrix.assay }} | |
| shell: pwsh | |
| env: | |
| TMPDIR: /tmp | |
| run: | | |
| pytest tests/test_pipelines.py::test_${{ matrix.test }}[${{ matrix.assay }}] -vv -s --cores 4 |