test_example.yml

name: Test example.sh

on:
  push:
    branches: [ "main", "dev" ]
  pull_request:
    branches: [ "main", "dev" ]

# Cancel if a newer run is started
# taken from https://github.com/nf-core/modules/blob/master/.github/workflows/nf-test.yml
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true


jobs:
  test:
    runs-on: ubuntu-latest
    steps:
    - name: Build msyd
      uses: schneebergerlab/msyd@main
      with:
        python-version: "3.12"
    - name: Install minimap2 manually # conda doesn't seem to work
      run: |
        curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar -jxvf -
        mv minimap2-2.28_x64-linux\/minimap2 ./
        ./minimap2 -h # test it worked & is callable
    - name: Test example_run.sh
      run: |
        $(tail -n +2 ./example/example_workflow.sh | sed -e 's/^syri/python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")/'  -e 's/^minimap2/.\/minimap2/' )
      shell: bash