Add SVCallers: gridss and CNV: cnvkit,ascat #63
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| pull_request: | |
| branches: | |
| - main | |
| - develop | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 2 | |
| strategy: | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Install nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| pip install .[dev,test] | |
| python -c 'from logan.src.util import chmod_bins_exec; chmod_bins_exec()' | |
| - name: Check CLI basics | |
| run: | | |
| which logan | |
| logan --version | |
| logan --citation | |
| - name: Test stub run for Fastqs | |
| run: | | |
| logan init | |
| logan run -profile ci_stub \ | |
| --sample_sheet .tests/pairs.tsv \ | |
| --fastq_input ".tests/*R{1,2}_001.fastq.gz" \ | |
| --vc --cnv --sv --gl --qc \ | |
| --split_regions 2 \ | |
| --genome hg38 \ | |
| --outdir output_tn_fqs \ | |
| --intervals .tests/interval.bed \ | |
| -stub | |