- name: scrubber-test-pe
  command: bash -c 'nextflow run ./subworkflows/local/scrubber/test.nf -entry test_scrubber_pe --wf scrubber -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - scrubber
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-dag.dot
      contains: ['scrubberdag', 'SRAHUMANSCRUBBER', 'versions']
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/SRR2838702_R1.scrubbed.fastq.gz
    - path: bactopia/SRR2838702/tools/srahumanscrubber/SRR2838702_R2.scrubbed.fastq.gz
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.err
      contains: ['aligns_to', 'FastaReader', 'total']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.log
      contains: ['aligns_to', 'FastaReader', 'total']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.sh
      contains: ['scrub', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/versions.yml
      md5sum: 6964d293234668d561237412de067eec

- name: scrubber-test-se
  command: bash -c 'nextflow run ./subworkflows/local/scrubber/test.nf -entry test_scrubber_se --wf scrubber -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - scrubber
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-dag.dot
      contains: ['scrubberdag', 'SRAHUMANSCRUBBER', 'versions']
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/SRR2838702.scrubbed.fastq.gz
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.err
      contains: ['aligns_to', 'FastaReader', 'total']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.log
      contains: ['aligns_to', 'FastaReader', 'total']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.sh
      contains: ['scrub', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/versions.yml
      md5sum: 7f879dc589c9f00beaf3551c06cc0b95
