Add virus configs #1026
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | |
| jobs: | |
| static_tests: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: false | |
| - name: Install conda environment dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-version: latest | |
| miniforge-variant: Mambaforge | |
| python-version: "3.11" | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda #,defaults # see: https://github.com/conda-forge/status/issues/144 | |
| channel-priority: strict | |
| activate-environment: V-pipe | |
| auto-update-conda: true | |
| environment-file: tests/conda_lint_env.yaml | |
| - name: Code formatting | |
| run: snakefmt --check . | |
| - name: Setup project | |
| run: | | |
| mkdir -p lintest/config # virus does not matter | |
| cd lintest/ | |
| $GITHUB_WORKSPACE/init_project.sh -n | |
| # dummy content so pipeline is configured properly | |
| cp -vr $GITHUB_WORKSPACE/tests/data/hiv/ ./samples | |
| sed -E 's/(#*virus_base_config:) .*$/\1 hiv/;s/false$/true/g;s/(trim_primers:) .*$/\1 false/' $GITHUB_WORKSPACE/config/config.yaml | tee ./config.yaml | |
| - name: Snakemake linting | |
| env: | |
| PYTHONUNBUFFERED: 1 | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: lintest/ | |
| snakefile: 'workflow/Snakefile' | |
| args: '--lint' | |
| continue-on-error: true # HACK for now snakemake linting is considered non-critical | |
| runtime_tests: | |
| needs: static_tests | |
| strategy: | |
| max-parallel: 5 | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.10", "3.11"] | |
| virus: ["hiv", "sars-cov-2"] | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: false | |
| # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS | |
| - name: Install conda environment dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-version: latest | |
| miniforge-variant: Mambaforge | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda #,defaults # see: https://github.com/conda-forge/status/issues/144 | |
| channel-priority: strict | |
| activate-environment: V-pipe | |
| auto-update-conda: true | |
| environment-file: tests/conda_test_env.yaml | |
| - name: Setup project | |
| run: | | |
| mkdir -p /tmp/project/${{ matrix.virus }}/ | |
| cd /tmp/project/${{ matrix.virus }}/ | |
| $GITHUB_WORKSPACE/init_project.sh -n | |
| - name: Run tests | |
| working-directory: ./tests | |
| run: ./regression_tests.sh ${{ matrix.virus }} | |
| - name: Archive code coverage results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: regression test output and diffs | |
| path: | | |
| /tmp/v-pipe_tests/* | |
| if-no-files-found: ignore |