- name: prokka-test
  command: bash -c 'nextflow run ./subworkflows/local/prokka/test.nf -entry test_prokka --wf prokka -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - prokka
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/prokka/nf-reports/prokka-dag.dot
      contains: ['prokkadag', 'PROKKA', 'versions']
    - path: bactopia/bactopia-runs/prokka/nf-reports/prokka-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/prokka/nf-reports/prokka-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/prokka/nf-reports/prokka-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685-blastdb.tar.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.faa.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.ffn.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.fna.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.fsa.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.gbk.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.gff.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.sqn.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.tbl.gz
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.tsv
      md5sum: 2b7d5a306fd8ffa44f5c1e9f2e3cce05
    - path: bactopia/GCF_000292685/main/annotator/prokka/GCF_000292685.txt
      md5sum: 09c05b70e569b8397697494b799fe2b0
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/GCF_000292685.err
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/GCF_000292685.log
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/nf-prokka.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/nf-prokka.err
      contains: ['prokka', 'finished', 'Torsten']
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/nf-prokka.log
      contains: ['prokka', 'finished', 'Torsten']
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/nf-prokka.out
      contains: ['tbl2asn-forever', 'changed', 'dates']
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/nf-prokka.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/nf-prokka.sh
      contains: ['prokka', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/nf-prokka.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/main/annotator/prokka/logs/versions.yml
      contains: ['prokka', 'makeblastdb']
