Merge pull request #16 from CCBR/python-cli #43
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| name: tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Stub_Run: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://nextflow/nextflow:22.10.8 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9' | |
| - name: Tumor-normal FastQ Stub Run | |
| run: | | |
| docker run -v $PWD:/opt2 nextflow/nextflow:22.10.8 \ | |
| python /opt2/wgs-seek --fastq "/opt2/.tests/*R{1,2}.fastq.gz" \ | |
| --mode vc \ | |
| --output /opt2/output_tn_fqs \ | |
| --paired --sample_sheet "/opt2/.tests/pairs.tsv" --stub | |
| - name: Tumor-only FastQ Stub Run | |
| run: | | |
| docker run -v $PWD:/opt2 nextflow/nextflow:22.10.8 \ | |
| python /opt2/wgs-seek --fastq "/opt2/.tests/*R{1,2}.fastq.gz" \ | |
| --mode vc \ | |
| --output "/opt2/output_tonly_fqs" --stub |