Fix multiallelic genotypes for biallelic CNVs #604
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| name: Test WDLs | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - 'wdl/**' | |
| - 'inputs/**' | |
| - 'scripts/inputs/build_default_inputs.sh' | |
| - 'scripts/test/terra_validation.py' | |
| - 'scripts/test/miniwdl_validation.py' | |
| - 'scripts/test/validate.sh' | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - 'wdl/**' | |
| - 'inputs/**' | |
| - 'scripts/inputs/build_default_inputs.sh' | |
| - 'scripts/test/terra_validation.py' | |
| - 'scripts/test/miniwdl_validation.py' | |
| - 'scripts/test/validate.sh' | |
| jobs: | |
| syntax_test_job: | |
| runs-on: ubuntu-22.04 | |
| name: Check WDL Syntax | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup Java | |
| uses: actions/setup-java@v3 | |
| with: | |
| # See https://github.com/actions/setup-java for the available options. | |
| distribution: 'temurin' | |
| java-version: '17' | |
| - name: Setup | |
| run: | | |
| python -m pip install --upgrade pip | |
| # Setup for running miniwdl | |
| pip install miniwdl | |
| # Setup for running womtool | |
| pip install jinja2==3.1.2 | |
| wget -O womtool.jar https://github.com/broadinstitute/cromwell/releases/download/84/womtool-84.jar | |
| scripts/inputs/build_default_inputs.sh -d . | |
| - name: Test with Miniwdl | |
| run: | | |
| python scripts/test/miniwdl_validation.py \ | |
| --imports-dir wdl \ | |
| wdl/*.wdl | |
| - name: Test with WOMtool | |
| run: | | |
| scripts/test/validate.sh -t -d . -j womtool.jar |