test_example.yml

name: Test example.sh

on:
  # do not run, as the conda package is currently broken,
  # making getting the right environment not possible.
  #  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: ./.github/workflows/run_test_example.sh
      shell: bash