test_assembler_all.yml

name: Test Donut Falls all assemblers

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: Download Unicycler test files
        run: |
          mkdir reads
          # from unicycler test data
          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz
          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz
          #wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_high_depth.fastq.gz
          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz

          mv *fastq.gz reads/.

      - name: Run Donut Falls
        run: |
          docker --version
          
          nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/github_actions_hybrid_sample_sheet.txt --assembler unicycler,flye,raven

          tree donut_falls

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