- name: agrvate-test
  command: bash -c 'nextflow run ./subworkflows/local/agrvate/test.nf -entry test_agrvate --wf agrvate -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - agrvate
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/agrvate/merged-results/agrvate.tsv
      contains: ['agr_group', 'GCF_000017085']
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/agrvate/merged-results/logs/agrvate-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/agrvate/nf-reports/agrvate-dag.dot
      contains: ['agrvatedag', 'AGRVATE', 'versions']
    - path: bactopia/bactopia-runs/agrvate/nf-reports/agrvate-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/agrvate/nf-reports/agrvate-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/agrvate/nf-reports/agrvate-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-agr_gp.tab
      md5sum: 04031d5b20fabcc4b3ddeef707e94029
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-blastn_log.txt
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-summary.tab
      md5sum: b483a3d6ca1908ab813427b06751e51a
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.err
      contains: ['download', 'usearch', 'mummer']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.log
      contains: ['agr', 'successful']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.out
      contains: ['agr', 'successful']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.sh
      contains: ['agrvate', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/versions.yml
      md5sum: c5fafc516992acaf78891c9df7b652df
