- name: abricate-test
  command: bash -c 'nextflow run ./subworkflows/local/abricate/test.nf -entry test_abricate --wf abricate -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - abricate
    - tools
  files:
    - path: bactopia/bactopia-runs/abricate/merged-results/abricate.tsv
      contains: ['FILE', 'NUM_FOUND']
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.begin
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.sh
      contains: ['abricate', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/versions.yml
      contains: ['abricate']
    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-dag.dot
      contains: ['abricatedag', 'ABRICATE', 'versions']
    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/abricate/GCF_000292685.txt
      contains: ['FILE', 'COVERAGE', 'RESISTANCE']
    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.err
      contains: ["database", "genes", "Done"]
    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.log
      contains: ["database", "genes", "Done"]
    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.sh
      contains: ['abricate', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/abricate/logs/versions.yml
      md5sum: 883068280465b2816cfae24f8ba0ec3c
