test v0.1.15 #38
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: assembly | |
| 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_assembly.sh | |
| bash scripts/unittests/unittest_assembly.sh |