Test pulling reference for construct vcf test #15
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| name: pytest | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pipenv codecov | |
| pip install -r requirements.txt | |
| pipenv install --dev | |
| - name: pull reference data | |
| run: | | |
| curl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz -o tests/test_data/hs37d5.fa.gz | |
| - name: gunzip data | |
| run: | | |
| gunzip tests/test_data/*.gz | |
| - name: Test with pytest | |
| run: | | |
| pytest -vv --cov . --cov scripts/ --cov utils/ |