- name: mykrobe-test
  command: bash -c 'nextflow run ./subworkflows/local/mykrobe/test.nf -entry test_mykrobe --wf mykrobe -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - mykrobe
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/mykrobe/merged-results/logs/mykrobe-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/mykrobe/merged-results/mykrobe.csv
      contains: ['sample', 'SRR2838702', 'Unknown']
    - path: bactopia/bactopia-runs/mykrobe/nf-reports/mykrobe-dag.dot
      contains: ['mykrobedag', 'MYKROBE', 'versions']
    - path: bactopia/bactopia-runs/mykrobe/nf-reports/mykrobe-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/mykrobe/nf-reports/mykrobe-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/mykrobe/nf-reports/mykrobe-trace.txt
      contains: ['task_id']
    - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.err
      contains: ['mykrobe', 'staph', 'finished']
    - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.log
      contains: ['mykrobe', 'staph', 'finished']
    - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.sh
      contains: ['mykrobe', 'END_VERSIONS']
    - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.trace
      contains: ['nextflow.trace']
    - path: bactopia/test/tools/mykrobe/logs/versions.yml
      md5sum: 9b226e8dcf0cbd7a9055291126babfd0
    - path: bactopia/test/tools/mykrobe/test.csv
      contains: ["susceptibility", "staph", "variants"]
    - path: bactopia/test/tools/mykrobe/test.json
      contains: ["susceptibility", "staph", "predictor"]
