name: "bracken_combinebrackenoutputs"
description: Combine output of metagenomic samples analyzed by bracken.
keywords:
  - sort
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 ]
  - input:
      type: file
      description: List of output files from bracken
      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"
  - txt:
      type: file
      description: Combined output in table format
      pattern: "*.txt"

authors:
  - "@jfy133"
