test_sample_sheet_lr_only.yml

name: Test Donut Falls sample sheet lr

on: [pull_request, workflow_dispatch]

jobs:

  test:
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout
        uses: actions/checkout@v4
            
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
 
      - name: Get files
        run: |
          wget --quiet https://zenodo.org/records/10779911/files/df_test_files.tar.gz?download=1 -O dataset.tar.gz
          tar -xvf dataset.tar.gz

          cp test_files/test_nanopore.fastq.gz test_files/test_nanopore_only.fastq.gz

      - name: Run Donut Falls
        run: |
          docker --version
          
          nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/sample_sheet_lr.csv

          tree donut_falls

      - name: Check files
        run: |
          ls  donut_falls/multiqc/multiqc_report.html
          cat donut_falls/summary/donut_falls_summary.json