capturing sambamba/markdup log for MultiQC report #1455
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| name: linux | |
| on: [pull_request, push] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| pip: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11', '3.12'] | |
| optdeps: [".", ".[actions]", ".[docs]"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: pip | |
| run: | | |
| pip install ${{ matrix.optdeps }} | |
| docs: | |
| needs: pip | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Install snakePipes | |
| run: | | |
| pip install .[docs] | |
| - name: docs | |
| run: | | |
| snakePipes config --tempDir /tmp | |
| cd docs | |
| make html | |
| lint: | |
| needs: pip | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Install snakePipes | |
| run: | | |
| pip install .[actions] | |
| - name: ruff | |
| run: | | |
| ruff check . | |
| CI: | |
| needs: pip | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: .github/conda_ci.yml | |
| activate-environment: conda_ci | |
| condarc-file: .github/condarc.yml | |
| - name: Install snakePipes | |
| run: | | |
| pip install . | |
| - name: print_conda_env_export | |
| run: | | |
| conda env export | |
| - name: print_pip_list | |
| run: | | |
| pip list | |
| - name: CI | |
| run: | | |
| snakePipes config --tempDir /tmp | |
| ./.ci_stuff/test_dag.sh | |
| createEnvs: | |
| needs: CI | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| envs: [ | |
| 'CONDA_SHARED_ENV', | |
| 'CONDA_CREATE_INDEX_ENV', | |
| 'CONDA_RNASEQ_ENV', | |
| 'CONDA_RMATS_ENV', | |
| 'CONDA_scRNASEQ_ENV', | |
| 'CONDA_seurat3_ENV', | |
| 'CONDA_loompy_ENV', | |
| 'CONDA_alevinqc_ENV', | |
| 'CONDA_eisaR_ENV', | |
| 'CONDA_DNA_MAPPING_ENV', | |
| 'CONDA_CHIPSEQ_ENV', | |
| 'CONDA_ATAC_ENV', | |
| 'CONDA_HIC_ENV', | |
| 'CONDA_WGBS_ENV', | |
| 'CONDA_DSS_ENV', | |
| 'CONDA_RMD_ENV', | |
| 'CONDA_PREPROCESSING_ENV', | |
| 'CONDA_NONCODING_RNASEQ_ENV', | |
| 'CONDA_SAMBAMBA_ENV', | |
| 'CONDA_pysam_ENV' | |
| ] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: .github/conda_ci.yml | |
| activate-environment: conda_ci | |
| condarc-file: .github/condarc.yml | |
| - name: install snakePipes | |
| run: | | |
| pip install . | |
| - name: createEnvs | |
| run: | | |
| snakePipes config --tempDir /tmp | |
| snakePipes createEnvs --only ${{matrix.envs}} |