Rename output files of bamtofastq not ending in '_001.fastq.gz' #208
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| name: Python Package using Conda | |
| on: [push] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: rnaseq-pipeline | |
| environment-file: environment.yml | |
| - name: Install package | |
| run: | | |
| pip install .[gsheet,webviewer] | |
| - name: Build shm cleanup script | |
| run: | | |
| make -C scripts | |
| - name: Configure the pipeline | |
| run: | | |
| cp example.luigi.cfg luigi.cfg | |
| - name: Test with pytest | |
| run: | | |
| conda install pytest | |
| pytest --ignore tests/test_webviewer.py |