update docs #31
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| name: quantification | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Free disk space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: false | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: test-env | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| # Remove tmp files | |
| sudo rm -rf /tmp/* | |
| # Install conda packages | |
| conda env list | |
| conda info | |
| conda config --add channels defaults | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| conda config --set channel_priority strict | |
| conda install pandas | |
| conda install nextflow==23.10.0 | |
| conda install pylint | |
| conda install coveralls | |
| conda install pytest | |
| conda install pytest-cov | |
| # Install nexus | |
| pip install . --verbose | |
| - name: Run linter | |
| shell: bash -l {0} | |
| run: | | |
| chmod +x lint.sh | |
| bash lint.sh | |
| - name: Run unit tests | |
| shell: bash -l {0} | |
| run: | | |
| chmod +x scripts/unittests/unittest_quantification.sh | |
| bash scripts/unittests/unittest_quantification.sh |