name: cutadapt
on:
  push: {}
  pull_request:
    paths: software/cutadapt/*

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

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

      - name: Test module with paired-end data
        run: |
          cd software/cutadapt/test_paired/
          nextflow run . -ansi-log false

      - name: Test module with single-end data
        run: |
          cd software/cutadapt/test_single/
          nextflow run . -ansi-log false