Filter out discriminatory taxa in utils.py, add in README that QADABRA is WIP software, add install from source instructions in README #97
Workflow file for this run
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| # github.com/snakemake-workflows/dna-seq-varlociraptor/blob/master/.github/workflows/main.yml | |
| name: "Main CI" | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| - develop | |
| paths-ignore: | |
| - "README.md" | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| paths-ignore: | |
| - "README.md" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: qadabra | |
| mamba-version: "*" | |
| channels: conda-forge,defaults,bioconda | |
| channel-priority: true | |
| python-version: "3.9" | |
| - name: Install conda packages | |
| shell: bash -l {0} | |
| run: mamba install snakemake click biom-format pandas numpy cython | |
| - name: Install pip packages | |
| shell: bash -l {0} | |
| run: pip install iow | |
| - name: Install qadabra | |
| shell: bash -l {0} | |
| run: pip install -e . | |
| - name: Run Snakemake | |
| shell: bash -l {0} | |
| run: make snaketest |