- name: genotyphi-test
  command: bash -c 'nextflow run ./subworkflows/local/genotyphi/test.nf -entry test_genotyphi --wf genotyphi -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - genotyphi
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/genotyphi/merged-results/genotyphi.tsv
      contains: ['genome', 'test', 'typhi']
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/genotyphi/nf-reports/genotyphi-dag.dot
      md5sum: 1b407e59487039bdbe295275cb4aef72
    - path: bactopia/bactopia-runs/genotyphi/nf-reports/genotyphi-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/genotyphi/nf-reports/genotyphi-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/genotyphi/nf-reports/genotyphi-trace.txt
      contains: ['task_id']
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/nf-genotyphi.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/nf-genotyphi.err
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/nf-genotyphi.log
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/nf-genotyphi.out
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/nf-genotyphi.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/nf-genotyphi.sh
      contains: ['parse', 'END_VERSIONS']
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/nf-genotyphi.trace
      contains: ['nextflow.trace']
    - path: bactopia/test/tools/genotyphi/logs/genotyphi/versions.yml
      md5sum: fa40b53652f6c0b23018061a816f23b3
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.err
      contains: ['mykrobe', 'typhi', 'finished']
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.log
      contains: ['mykrobe', 'typhi', 'finished']
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.out
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.sh
      contains: ['mykrobe', 'END_VERSIONS']
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.trace
      contains: ['nextflow.trace']
    - path: bactopia/test/tools/genotyphi/logs/mykrobe/versions.yml
      md5sum: 82aff618ee15aa872566d48a3c527437
    - path: bactopia/test/tools/genotyphi/test.csv
      contains: ["susceptibility", "typhi", "variants"]
    - path: bactopia/test/tools/genotyphi/test.json
      contains: ["susceptibility", "typhi", "predictor"]
    - path: bactopia/test/tools/genotyphi/test_predictResults.tsv
      contains: ['genome', 'test', 'typhi']
