wes and wgs samples in hail search #530
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| name: Hail Search Unit Tests | |
| # Run the test suite on pushes (incl. merges) to master and dev | |
| # Run the test suite when a PR is opened, pushed to, or reopened | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| paths: | |
| - 'hail_search/**' | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| paths: | |
| - 'hail_search/**' | |
| jobs: | |
| hail_search: | |
| runs-on: ubuntu-latest | |
| container: hailgenetics/hail:0.2.128 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip wheel | |
| pip install -r hail_search/requirements-test.txt | |
| - name: Run coverage tests | |
| run: | | |
| export HAIL_SEARCH_DATA_DIR=./hail_search/fixtures | |
| export REFERENCE_DATASETS_DIR=./hail_search/fixtures/reference_data | |
| export MAX_GENE_INTERVALS=3 | |
| export MACHINE_MEM=24 | |
| export JAVA_OPTS_XSS=16M | |
| coverage run --source="./hail_search" --omit="./hail_search/__main__.py","./hail_search/test_utils.py" -m pytest hail_search/ | |
| coverage report --fail-under=99 |