Merge pull request #157 from polio-nanopore/phylo-dev #342
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| name: piranha | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| run_piranha_test: | |
| name: piranha test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment.yml | |
| activate-environment: piranha | |
| channels: conda-forge,bioconda,defaults | |
| conda-version: "23.5.0" | |
| mamba-version: "*" | |
| - name: Install piranha | |
| run: pip install -e . | |
| - name: Check piranha version | |
| run: piranha --version | |
| - name: Run piranha with test data | |
| run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 2>&1 | tee piranha.log | |
| - name: Run piranha with all data | |
| run: piranha -i piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes.csv -t 2 2>&1 | tee piranha_all.log |