test_pr_hybrid_docker.yml

name: Testing hybrid / docker from PR
on:
  pull_request:
    branches: [master, dev]
    types: [opened, synchronize, reopened]

jobs:
  run_nextflow:
    name: Run pipeline for the upcoming PR
    runs-on: ubuntu-latest

    steps:

    - name: Check out pipeline code
      uses: actions/checkout@v2

    - name: Install Nextflow
      env:
        CAPSULE_LOG: none
      run: |
        wget -qO- get.nextflow.io | bash
        sudo mv nextflow /usr/local/bin/

    - name: Clean environment
      run: |
        sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
        sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET

    - name: Run tests for hybrid
      run: |
        nextflow run main.nf -profile docker,test,hybrid,pacbio --skip_haslr
        rm -r work .nextflow*

    - name: View results
      run: |
        sudo apt-get install -y tree
        tree hybrid_test_pacbio