log: add warning for no g2a used together with rescale #210
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name: pydamage_ci | |
on: [push, pull_request] | |
jobs: | |
pydamage_ci: | |
name: pydamage_testing | |
runs-on: 'ubuntu-latest' | |
if: "!contains(github.event.head_commit.message, '[skip_ci]')" | |
steps: | |
- uses: actions/checkout@v2 | |
- uses: conda-incubator/setup-miniconda@v3 | |
with: | |
auto-update-conda: true | |
mamba-version: "*" | |
channels: conda-forge,bioconda,defaults | |
channel-priority: true | |
environment-file: environment.yml | |
activate-environment: pydamage | |
- name: Test with pytest | |
shell: bash -l {0} | |
run: | | |
pip install -e . | |
pip install pytest | |
pytest | |
- name: Check pydamage help message | |
shell: bash -l {0} | |
run: | | |
pydamage --help | |
- name: Check pydamage on test data | |
shell: bash -l {0} | |
run: | | |
pydamage analyze --verbose tests/data/aligned.bam | |
pydamage filter pydamage_results/pydamage_results.csv | |
pydamage analyze -f -g tests/data/aligned.bam | |
pydamage cite |