- name: kleborate-test
  command: bash -c 'nextflow run ./subworkflows/local/kleborate/test.nf -entry test_kleborate --wf kleborate -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - kleborate
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/kleborate/merged-results/kleborate.tsv
      contains: ['strain', 'GCF_000009885']
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/kleborate/merged-results/logs/kleborate-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/kleborate/nf-reports/kleborate-dag.dot
      contains: ['kleboratedag', 'KLEBORATE', 'versions']
    - path: bactopia/bactopia-runs/kleborate/nf-reports/kleborate-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/kleborate/nf-reports/kleborate-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/kleborate/nf-reports/kleborate-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000009885/tools/kleborate/GCF_000009885.results.txt
      contains: ['strain', 'GCF_000009885']
    - path: bactopia/GCF_000009885/tools/kleborate/logs/nf-kleborate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000009885/tools/kleborate/logs/nf-kleborate.err
    - path: bactopia/GCF_000009885/tools/kleborate/logs/nf-kleborate.log
      contains: ['strain', 'GCF_000009885']
    - path: bactopia/GCF_000009885/tools/kleborate/logs/nf-kleborate.out
      contains: ['strain', 'GCF_000009885']
    - path: bactopia/GCF_000009885/tools/kleborate/logs/nf-kleborate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000009885/tools/kleborate/logs/nf-kleborate.sh
      contains: ['kleborate', 'END_VERSIONS']
    - path: bactopia/GCF_000009885/tools/kleborate/logs/nf-kleborate.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000009885/tools/kleborate/logs/versions.yml
      md5sum: 041d3867387e9cdb927b06ed8c93b25b
