name: bracken_bracken
description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
keywords:
  - bracken
  - metagenomics
  - abundance
  - kraken2
tools:
  - bracken:
      description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
      homepage: https://ccb.jhu.edu/software/bracken/
      documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
      tool_dev_url: https://github.com/jenniferlu717/Bracken
      doi: "10.7717/peerj-cs.104"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - kraken_report:
      type: file
      description: TSV file with six columns coming from kraken2 output
      pattern: "*.{tsv}"
  - database:
      type: file
      description: Directory containing the kraken2/Bracken files for analysis
      pattern: "*"

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"
  - reports:
      type: file
      description: TSV output report of the re-estimated abundances
      pattern: "*.{tsv}"
  - txt:
      type: file
      description: TXT file of bracken corrected results of Kraken2 report output
      pattern: "*.txt"

authors:
  - "@Midnighter"
