name: kleborate
description: Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC).
keywords:
  - screening assemblies
  - Klebsiella pneumoniae
tools:
  - kleborate:
      description: Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest
      homepage: https://github.com/katholt/Kleborate
      documentation: https://github.com/katholt/Kleborate/wiki
      tool_dev_url: https://github.com/katholt/Kleborate
      doi: 10.1038/s41467-021-24448-3
      licence: ['GPL v3 or later (GPL v3+)']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastas:
      type: files
      description: Klebsiella genome assemblies to be screened
      pattern: "*.fasta"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - txt:
      type: file
      description: Result file generated after screening
      pattern: "*.txt"

authors:
  - "@abhi18av"
  - "@rpetit3"