integration_tests.yml

name: Run Integration Tests

on:
  push:

  pull_request:
    types: [opened, reopened]

jobs:
  build:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    env:
      CRISPRESSO2_DIR: ${GITHUB_WORKSPACE}/../CRISPResso2_copy

    strategy:
      fail-fast: false

    steps:
    - uses: actions/checkout@v3

    - name: Set up Conda
      uses: conda-incubator/setup-miniconda@v2
      with:
          mamba-version: "*"
          channels: conda-forge,bioconda,defaults
          auto-activate-base: false
          activate-environment: test_env
          environment-file: .github/envs/test_env.yml

    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
        pip install ydiff

    - name: Create directory for files
      run: |
        mkdir ../CRISPResso2_copy
        cp -r * ../CRISPResso2_copy

    - name: Copy C2_tests repo
      uses: actions/checkout@v3
      with:
        repository: edilytics/CRISPResso2_tests
        token: ${{ secrets.ACCESS_CRISPRESSO2_TESTS }}
        # ref: '<BRANCH_NAME>' // Use this to specify a branch other than master

    - name: Run Basic
      run: |
        make basic test

    - name: Run Params
      if: success() || failure()
      run: |
        make params test

    - name: Run Prime Editor
      if: success() || failure()
      run: |
        make prime-editor test

    - name: Run Batch
      if: success() || failure()
      run: |
        make batch test

    - name: Run Pooled
      if: success() || failure()
      run: |
        make pooled test

    - name: Run WGS
      if: success() || failure()
      run: |
        make wgs test

    - name: Run Compare
      if: success() || failure()
      run: |
        make compare test