Set pipefail #160
Workflow file for this run
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| name: Variant Remapping | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| # Install dependencies | |
| sudo apt-get install libgsl0-dev | |
| # Install Nextflow | |
| mkdir /tmp/nextflow && cd /tmp/nextflow | |
| wget -qO- get.nextflow.io | bash | |
| echo "/tmp/nextflow" >> $GITHUB_PATH | |
| cd - | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| $CONDA/bin/conda update conda | |
| $CONDA/bin/conda install -y python=${{ matrix.python-version }} | |
| $CONDA/bin/conda env update -q --file conda.yml --name base | |
| $CONDA/bin/conda run pip install -q -r requirements.txt | |
| - name: Test nextflow workflow | |
| run: | | |
| $CONDA/bin/conda run tests/test_pipeline.sh | |
| $CONDA/bin/conda run tests/test_pipeline_empty.sh | |
| - name: Test with pytest | |
| run: | |
| $CONDA/bin/conda run PYTHONPATH=. pytest variant_remapping_tools/tests |