name: FastQC
on:
  push: {}
  pull_request:
    paths: tools/tcoffee/*

jobs:
  run_ci_test:
    runs-on: ubuntu-latest

    steps:

    # Check out the repository
    - uses: actions/checkout@v2
    - name: Checkout submodules
      shell: bash
      run: |
          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
          git submodule sync --recursive
          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
          ls -la test-datasets/tools/tcoffee/input/
          echo "============"
          rm ./test-datasets/tools/tcoffee/input/BBA0001.tfa
          cp test-datasets/general/fasta/msa/BBA0001.tfa ./test-datasets/tools/tcoffee/input/

    - name: Install Nextflow
      run: |
        wget -qO- get.nextflow.io | bash
        sudo mv nextflow /usr/local/bin/

    # Test the module
    - run: nextflow run ./tools/tcoffee/test/ -ansi-log false