main.yml

name: CI
on: [push]
jobs:
  build-and-test:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: false
          use-only-tar-bz2: true
          miniforge-version: latest
      - name: Install cnv_facets
        run: |
          mamba init
          source ~/.bashrc
          mamba create --yes -n cnv_facets
          mamba activate cnv_facets
          mamba install --yes -c bioconda -c conda-forge cnv_facets
      - name: Install vcf_validator
        run: |
          curl -L -o test/vcf_validator -s https://github.com/EBIvariation/vcf-validator/releases/download/v0.9.1/vcf_validator_linux
          chmod a+x test/vcf_validator
          ./test/vcf_validator --help
      - name: Run tests
        run: |
          source ~/.bashrc
          mamba activate cnv_facets
          cd test
          Rscript testthat.R
          python3 test_cnv_facets.py