Merge pull request #49 from yangchen2/master #93
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |