fix edits #111
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| name: denv_pipeline | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| run_pipeline_tests: | |
| name: analysis_pipeline test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment.yml | |
| activate-environment: analysis_env | |
| channels: conda-forge,bioconda,defaults | |
| miniconda-version: "latest" | |
| - name: install pipeline | |
| run: pip install -e . | |
| - name: run_dry_run | |
| working-directory: tests | |
| run: denv_pipeline --config dry_run_config.yml --dry-run | |
| - name: test_setup | |
| working-directory: tests | |
| run: python scripts/unit_tests_dry_run.py | |
| \--in-config dry_run_config.yml | |
| \--out-config test_output_dry_run/output_config.yml | |
| \--outdir test_output_dry_run | |
| - name: install snakemake dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: run_full | |
| working-directory: tests | |
| run: denv_pipeline --config base_run_config.yml | |
| - name: test_results | |
| working-directory: tests | |
| run: python scripts/unit_tests_results.py | |
| \--outdir test_output_full_run/results | |
| \--depth 10 | |