- name: emmtyper-test
  command: bash -c 'nextflow run ./subworkflows/local/emmtyper/test.nf -entry test_emmtyper --wf emmtyper -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - emmtyper
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/emmtyper/merged-results/emmtyper.tsv
      md5sum: 38f46cf186d95a5602ff33144a3b105e
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/emmtyper/merged-results/logs/emmtyper-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/emmtyper/nf-reports/emmtyper-dag.dot
      contains: ['emmtyperdag', 'EMMTYPER', 'versions']
    - path: bactopia/bactopia-runs/emmtyper/nf-reports/emmtyper-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/emmtyper/nf-reports/emmtyper-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/emmtyper/nf-reports/emmtyper-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_006364235/tools/emmtyper/GCF_006364235.tsv
      md5sum: 38f46cf186d95a5602ff33144a3b105e
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/nf-emmtyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/nf-emmtyper.err
      contains: ['emmtyper', 'Finished']
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/nf-emmtyper.log
      contains: ['emmtyper', 'Finished']
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/nf-emmtyper.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/nf-emmtyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/nf-emmtyper.sh
      contains: ['emmtyper', 'END_VERSIONS']
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/nf-emmtyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_006364235/tools/emmtyper/logs/versions.yml
      md5sum: c524713d81202cd6a9d891f346175a8c
