Merge pull request #61 from TRON-Bioinformatics/56_add_mamba_support #188
Workflow file for this run
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| name: Automated tests | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'zulu' # See 'Supported distributions' for available options | |
| java-version: '11' | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| - name: Install dependencies | |
| run: | | |
| apt-get update && apt-get --assume-yes install wget build-essential procps software-properties-common libgsl0-dev | |
| wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow | |
| pip install virtualenv | |
| - name: Cache conda environments | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| /home/runner/work/covigator-ngs-pipeline/covigator-ngs-pipeline/work/conda | |
| key: ${{ runner.os }}-covigator-ngs-pipeline | |
| - name: Run tests | |
| run: | | |
| export NXF_VER=22.04.5 | |
| make |