Only run the annotation and the stats for analysis or the whole study #922
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9] | |
| nextflow-version: [21.10.5, 22.10.7] | |
| java-version: [11] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Java ${{ matrix.java-version }} | |
| uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '${{ matrix.java-version }}' | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies ${{ matrix.nextflow-version }} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| python setup.py install | |
| # Install Nextflow | |
| mkdir /tmp/nextflow && cd /tmp/nextflow | |
| wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v${{ matrix.nextflow-version }}/nextflow-${{ matrix.nextflow-version }}-all | bash | |
| echo "/tmp/nextflow" >> $GITHUB_PATH | |
| cd - | |
| # Build java dependencies | |
| tests/nextflow-tests/build_tests.sh | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| # reduce the default SSL security level to get around a misconfiguration in the Ensembl server | |
| # https://github.com/Ensembl/ensembl-rest/issues/427 | |
| # See https://askubuntu.com/a/1233456 | |
| sed 's/DEFAULT@SECLEVEL=2/DEFAULT@SECLEVEL=1/' /usr/lib/ssl/openssl.cnf > openssl_sec1.cnf | |
| export OPENSSL_CONF=openssl_sec1.cnf | |
| PYTHONPATH=. pytest tests | |
| - name: Test nextflow workflows | |
| run: | | |
| # Run nextflow tests | |
| tests/nextflow-tests/run_tests_validation.sh | |
| tests/nextflow-tests/run_tests_prep_brokering.sh | |
| tests/nextflow-tests/run_tests_accession_and_variant_load.sh | |
| tests/nextflow-tests/run_tests_accession_and_variant_load_human.sh | |
| tests/nextflow-tests/run_tests_clustering.sh | |
| tests/nextflow-tests/run_tests_remapping_clustering.sh |