EVA-3430 - Add bcftools norm before ingesting (#25) #183
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| # This workflow will install Python dependencies, run tests and lint for Python scripts | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Covid-19 DP submission CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| java-version: [1.11] | |
| python-version: [3.8] | |
| vcf-validator-version: [0.9.4] | |
| mongo-version: [4.0.21] | |
| services: | |
| db: | |
| image: postgres | |
| env: | |
| POSTGRES_DB: postgres | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| ports: | |
| - 5432:5432 | |
| mongodb: | |
| image: mongo:${{ matrix.mongo-version }} | |
| ports: | |
| - 27017:27017 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Java JDK # Nextflow relies on JDK | |
| uses: actions/[email protected] | |
| # The Java version to make available on the path. Takes a whole or semver Java version, or 1.x syntax (e.g. 1.8 => Java 8.x). Early access versions can be specified in the form of e.g. 14-ea, 14.0.0-ea, or 14.0.0-ea.28 | |
| with: | |
| java-version: ${{ matrix.java-version }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| python setup.py install | |
| - name: Set up Nextflow | |
| run: | | |
| sudo bash -c "export JAVA_CMD="$(which java)" && cd /usr/bin && (curl -s https://get.nextflow.io | bash) && chmod 755 nextflow" | |
| /usr/bin/nextflow -version | |
| - name: Set up VCF validator and assembly checker | |
| run: | | |
| sudo bash -c "cd /usr/bin && wget https://github.com/EBIvariation/vcf-validator/releases/download/v${{ matrix.vcf-validator-version }}/vcf_validator_linux && chmod 755 vcf_validator_linux" | |
| sudo bash -c "cd /usr/bin && wget https://github.com/EBIvariation/vcf-validator/releases/download/v${{ matrix.vcf-validator-version }}/vcf_assembly_checker_linux && chmod 755 vcf_assembly_checker_linux" | |
| - name: Set up BCFtools | |
| run: | | |
| sudo apt update | |
| sudo apt -y install maven samtools bcftools parallel libbz2-dev liblzma-dev | |
| - name: Set up ascp binary | |
| # Might need to periodically update this URL | |
| run: | | |
| curl https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect_4.1.3.93_linux.tar.gz -o ibm-aspera-connect.tar.gz | |
| tar xzvf ibm-aspera-connect.tar.gz | |
| ./ibm-aspera-connect_*_linux.sh | |
| chmod +x ~/.aspera/connect/bin/ascp; sudo ln -s ~/.aspera/connect/bin/ascp /usr/bin | |
| - name: Test with pytest | |
| env: | |
| EVA_STATS_DEV_PASSWORD: ${{ secrets.EVA_STATS_DEV_PASSWORD }} | |
| run: | | |
| export ASPERA_ID_DSA=~/.aspera/connect/etc/asperaweb_id_dsa.openssh | |
| PYTHONPATH=. pytest tests | |
| - name: Test bash script | |
| run: | | |
| tests/test_run_ingestion.sh |