- name: scoary-test
  command: bash -c 'nextflow run ./subworkflows/local/scoary/test.nf -entry test_scoary --wf scoary -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - scoary
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/scoary/nf-reports/scoary-dag.dot
      contains: ['scoarydag', 'SCOARY', 'versions']
    - path: bactopia/bactopia-runs/scoary/nf-reports/scoary-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/scoary/nf-reports/scoary-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/scoary/nf-reports/scoary-trace.txt
      contains: ['task_id']
    - path: bactopia/bactopia-runs/scoary/scoary/Bogus_trait.results.csv
      md5sum: a55a7783b0881627d32288222fa44b38
    - path: bactopia/bactopia-runs/scoary/scoary/Tetracycline_resistance.results.csv
      md5sum: a55a7783b0881627d32288222fa44b38
    - path: bactopia/bactopia-runs/scoary/scoary/logs/nf-scoary.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/scoary/scoary/logs/nf-scoary.err
    - path: bactopia/bactopia-runs/scoary/scoary/logs/nf-scoary.log
      contains: ["Performing", "Tallying", "Storing", "finished"]
    - path: bactopia/bactopia-runs/scoary/scoary/logs/nf-scoary.out
      contains: ["Performing", "Tallying", "Storing", "finished"]
    - path: bactopia/bactopia-runs/scoary/scoary/logs/nf-scoary.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/scoary/scoary/logs/nf-scoary.sh
      contains: ['scoary', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/scoary/scoary/logs/nf-scoary.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/scoary/scoary/logs/scoary.log
      contains: ["Performing", "Tallying", "Storing", "finished"]
    - path: bactopia/bactopia-runs/scoary/scoary/logs/versions.yml
      md5sum: 1bc3a23cae80f7cb9debb58b513d28fc
