Merge pull request #61 from TRON-Bioinformatics/56_add_mamba_support #191
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
| 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 |