Merge pull request #86 from AfshinLab/fix-85 #519
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| name: CI | |
| on: | |
| push: | |
| branch: | |
| - main | |
| pull_request: | |
| branch: | |
| - main | |
| schedule: | |
| - cron: 0 7 10 * * | |
| jobs: | |
| Linting: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.6 | |
| architecture: x64 | |
| - name: Install flake8 | |
| run: | |
| pip install flake8 | |
| - name: Run flake8 | |
| run: | | |
| flake8 src/ tests/ | |
| flake8 --select=W292 --filename '*.yaml,*.yml' | |
| Testing: | |
| needs: | |
| - Linting | |
| name: Run pipeline | |
| timeout-minutes: 15 | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| environment-file: environment.linux-64.lock | |
| - name: Install test deps | |
| run: | | |
| mamba install pytest | |
| # Bioconda build for deepvariant no working currently | |
| # see: | |
| # - https://github.com/bioconda/bioconda-recipes/issues/30310 | |
| # - https://github.com/nf-core/modules/issues/1754 | |
| # mamba install deepvariant=1.3.0 | |
| - name: Install BLR | |
| run: pip install . | |
| - name: Download test dataset | |
| env: | |
| testdata_version: "0.7" | |
| run: | | |
| wget -nv https://export.uppmax.uu.se/uppstore2018173/blr-testdata-${testdata_version}.tar.gz | |
| tar xf blr-testdata-${testdata_version}.tar.gz | |
| ln -s blr-testdata-${testdata_version} blr-testdata | |
| - name: Run tests | |
| run: | | |
| tests/run.sh |