update xlsx #7
Workflow file for this run
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| name: Integration Tests | |
| on: | |
| pull_request: | |
| branches: [master] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies & package | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt -r requirements-dev.txt | |
| python setup.py install | |
| - name: Test download of databases | |
| run: fusion_report download --cosmic_usr "${{ secrets.COSMIC_USERNAME }}" --cosmic_passwd "${{ secrets.COSMIC_PASSWD }}" ./db | |
| - name: Test run | |
| run: | | |
| fusion_report run "example-sample" ./docs/example ./db/ \ | |
| --arriba tests/test_data/arriba.tsv \ | |
| --fusioncatcher tests/test_data/fusioncatcher.txt \ | |
| --starfusion tests/test_data/starfusion.tsv \ | |
| --export csv |