- name: pneumocat-test
  command: bash -c 'nextflow run ./subworkflows/local/pneumocat/test.nf -entry test_pneumocat --wf pneumocat -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - pneumocat
    - bactopia-tools
  files:
    - path: bactopia/ERR1438863/tools/pneumocat/ERR1438863.results.xml
      md5sum: a9d9d8db3cbeff3f45859bed7eadaf9b
    - path: bactopia/ERR1438863/tools/pneumocat/coverage_summary.txt
      md5sum: 72016a38b82c726548cf5b58794c4938
    - path: bactopia/ERR1438863/tools/pneumocat/logs/nf-pneumocat.begin
    - path: bactopia/ERR1438863/tools/pneumocat/logs/nf-pneumocat.err
    - path: bactopia/ERR1438863/tools/pneumocat/logs/nf-pneumocat.log
      contains: ['bowtie']
    - path: bactopia/ERR1438863/tools/pneumocat/logs/nf-pneumocat.out
      contains: ['bowtie']
    - path: bactopia/ERR1438863/tools/pneumocat/logs/nf-pneumocat.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/ERR1438863/tools/pneumocat/logs/nf-pneumocat.sh
      md5sum: 5bd69dbe12701c939a222a69b5da6518
    - path: bactopia/ERR1438863/tools/pneumocat/logs/nf-pneumocat.trace
      contains: ['nextflow.trace']
    - path: bactopia/ERR1438863/tools/pneumocat/logs/versions.yml
      md5sum: a142274035f6b258122e4863a90eb64f
    - path: bactopia/bactopia-runs/pneumocat/nf-reports/pneumocat-dag.dot
      contains: ['pneumocatdag', 'PNEUMOCAT', 'versions']
    - path: bactopia/bactopia-runs/pneumocat/nf-reports/pneumocat-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/pneumocat/nf-reports/pneumocat-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/pneumocat/nf-reports/pneumocat-trace.txt
      contains: ['task_id']
