automated_tests.yml

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