- name: pbptyper-test
  command: bash -c 'nextflow run ./subworkflows/local/pbptyper/test.nf -entry test_pbptyper --wf pbptyper -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - pbptyper
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/pbptyper/merged-results/logs/pbptyper-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/pbptyper/merged-results/pbptyper.tsv
      md5sum: 0e01467865b2bcd76d597dc76e108d12
    - path: bactopia/bactopia-runs/pbptyper/nf-reports/pbptyper-dag.dot
      contains: ['pbptyperdag', 'PBPTYPER', 'versions']
    - path: bactopia/bactopia-runs/pbptyper/nf-reports/pbptyper-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/pbptyper/nf-reports/pbptyper-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/pbptyper/nf-reports/pbptyper-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_001457635/tools/pbptyper/GCF_001457635-1A.tblastn.tsv
      contains: ['qseqid', 'NZ_LN831051.1', 'SPN_1A']
    - path: bactopia/GCF_001457635/tools/pbptyper/GCF_001457635-2B.tblastn.tsv
      contains: ['qseqid', 'NZ_LN831051.1', 'SPN_2B']
    - path: bactopia/GCF_001457635/tools/pbptyper/GCF_001457635-2X.tblastn.tsv
      contains: ['qseqid', 'NZ_LN831051.1', 'SPN_2X']
    - path: bactopia/GCF_001457635/tools/pbptyper/GCF_001457635.tsv
      md5sum: 0e01467865b2bcd76d597dc76e108d12
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/nf-pbptyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/nf-pbptyper.err
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/nf-pbptyper.log
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/nf-pbptyper.out
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/nf-pbptyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/nf-pbptyper.sh
      contains: ['pbptyper', 'END_VERSIONS']
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/nf-pbptyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_001457635/tools/pbptyper/logs/versions.yml
      md5sum: 48de37dae1bb2c2c7f0f444887f753c6
