name: kaiju_kaiju2krona
description: Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona.
keywords:
  - taxonomy
  - visualisation
  - krona chart
  - metagenomics
tools:
  - "kaiju":
      description: Fast and sensitive taxonomic classification for metagenomics
      homepage: https://kaiju.binf.ku.dk/
      documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
      tool_dev_url: https://github.com/bioinformatics-centre/kaiju
      doi: "10.1038/ncomms11257"
      licence: ["GNU GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - tsv:
      type: file
      description: Kaiju tab-separated output file
      pattern: "*.{tsv,txt}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - txt:
      type: file
      description: Krona text-based input file converted from Kaiju report
      pattern: "*.{txt,krona}"

authors:
  - "@MillironX"