name: "kaiju_kaiju2table"
description: write your description here
keywords:
  - classify
  - 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 ]
  - results:
      type: file
      description: File containing the kaiju classification results
      pattern: "*.{txt}"
  - taxon_rank:
      type: string
      description: |
        Taxonomic rank to display in report
        pattern: "phylum|class|order|family|genus|species"

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"
  - results:
      type: file
      description: |
        Summary table for a given taxonomic rank
      pattern: "*.{tsv}"

authors:
  - "@sofstam"
  - "@talnor"
  - "@jfy133"