- name: shigeifinder-test
  command: bash -c 'nextflow run ./subworkflows/local/shigeifinder/test.nf -entry test_shigeifinder --wf shigeifinder -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - shigeifinder
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/logs/shigeifinder-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/shigeifinder/merged-results/shigeifinder.tsv
      md5sum: 25be6cf1161e59d9a4eab8db8f9b9ebb
    - path: bactopia/bactopia-runs/shigeifinder/nf-reports/shigeifinder-dag.dot
      contains: ['shigeifinder', 'SHIGEIFINDER', 'versions']
    - path: bactopia/bactopia-runs/shigeifinder/nf-reports/shigeifinder-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/shigeifinder/nf-reports/shigeifinder-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/shigeifinder/nf-reports/shigeifinder-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_016726285/tools/shigeifinder/GCF_016726285.tsv
      md5sum: aa4996a8f1027de2483b70687c0e8f00
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/nf-shigeifinder.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/nf-shigeifinder.err
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/nf-shigeifinder.log
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/nf-shigeifinder.out
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/nf-shigeifinder.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/nf-shigeifinder.sh
      contains: ['shigeifinder', 'END_VERSIONS']
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/nf-shigeifinder.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_016726285/tools/shigeifinder/logs/versions.yml
      md5sum: b678d07e56355d1a478a94c4308c5c7b
