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Create temp directory into output directory and download there #3

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Create temp directory into output directory and download there

Create temp directory into output directory and download there #3

Workflow file for this run

.github/workflows/integration_tests.yml at e264a4c
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