HiC outdirs in tests to factory too #1300
Workflow file for this run
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: linux | |
| on: [pull_request, push] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| activate-environment: snakePipes_CI | |
| condarc-file: .github/condarc.yml | |
| - name: Install snakePipes | |
| run: | | |
| pip install .[docs] | |
| - name: docs | |
| run: | | |
| snakePipes config --tempDir /tmp | |
| cd docs | |
| make html | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| activate-environment: snakePipes_CI | |
| condarc-file: .github/condarc.yml | |
| - name: Install snakePipes | |
| run: | | |
| pip install .[actions] | |
| - name: ruff | |
| run: | | |
| ruff check . | |
| CI: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| activate-environment: snakePipes_CI | |
| condarc-file: .github/condarc.yml | |
| - name: Install snakePipes | |
| run: | | |
| pip install . | |
| - 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/snakePipesEnvCI.yml | |
| activate-environment: snakePipes_CI | |
| condarc-file: .github/condarc.yml | |
| - name: install snakePipes | |
| run: | | |
| pip install . | |
| - name: createEnvs | |
| run: | | |
| snakePipes config --tempDir /tmp | |
| snakePipes createEnvs --only ${{matrix.envs}} |