variant_remapping.yml

name: Variant Remapping

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.8]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        # Install dependencies
        sudo apt-get install libgsl0-dev
        # Install Nextflow
        mkdir /tmp/nextflow && cd /tmp/nextflow
        wget -qO- get.nextflow.io | bash
        echo "/tmp/nextflow" >> $GITHUB_PATH
        cd -
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        $CONDA/bin/conda update conda                                    # https://github.com/conda/conda/issues/13560
        $CONDA/bin/conda install -y python=${{ matrix.python-version }}  # https://github.com/actions/setup-python/issues/833
        $CONDA/bin/conda env update -q --file conda.yml --name base
        $CONDA/bin/conda run pip install -q -r requirements.txt

    - name: Test nextflow workflow
      run: |
        $CONDA/bin/conda run tests/test_pipeline.sh
        $CONDA/bin/conda run tests/test_pipeline_empty.sh

    - name: Test with pytest
      run:
        $CONDA/bin/conda run PYTHONPATH=. pytest variant_remapping_tools/tests