test.yml

name: test

on:
  push:
    branches:
      - before_read_from_file_commit
  pull_request:
    branches:
      - before_read_from_file_commit

jobs:
  test:
    runs-on: ubuntu-latest

    steps:
    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y samtools
        sudo apt-get install -y nextflow
        sudo apt-get install -y tr
        sudo apt-get install -y gzip

      - name: Setup miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          # miniforge-variant: Mambaforge
          channels: conda-forge, bioconda, defaults
          auto-activate-base: true
          use-mamba: true
      - name: Checkout code
        uses: actions/checkout@v4
      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v2.0.0
      - name: Run test script
        run: |
          sudo apt-get install -y libxml2-utils samtools
          bash run_test.sh