- name: plasmidfinder-test
  command: bash -c 'nextflow run ./subworkflows/local/plasmidfinder/test.nf -entry test_plasmidfinder --wf plasmidfinder -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - plasmidfinder
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/plasmidfinder/merged-results/plasmidfinder.tsv
      md5sum: 7aa17dc82d1efd058422d8e0cc45db1a
    - path: bactopia/bactopia-runs/plasmidfinder/nf-reports/plasmidfinder-dag.dot
      contains: ['plasmidfinderdag', 'PLASMIDFINDER', 'versions']
    - path: bactopia/bactopia-runs/plasmidfinder/nf-reports/plasmidfinder-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/plasmidfinder/nf-reports/plasmidfinder-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/plasmidfinder/nf-reports/plasmidfinder-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085-hit_in_genome_seq.fsa
      md5sum: aa23c76c32c24285e8466c31cddb837c
    - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085-plasmid_seqs.fsa
      md5sum: ba224a3b41f1d92a915f3b3b5a10890d
    - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085.json
      contains: ["plasmidfinder", "results", "RepA", "GCF_000017085"]
    - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085.tsv
      md5sum: 7aa17dc82d1efd058422d8e0cc45db1a
    - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085.txt
      contains: ['Results', 'Plasmid', 'Query', 'template']
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.err
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.log
      contains: ["Found", "plasmid", "RepA", "GCF_000017085"]
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.out
      contains: ["Found", "plasmid", "RepA", "GCF_000017085"]
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.sh
      contains: ['plasmidfinder', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/versions.yml
      md5sum: a3b2229941f932b50690a1438fb909c7
