name: krakentools_combinekreports
description: Takes a Kraken report file and prints out a krona-compatible TEXT file
keywords:
  - kraken
  - krakentools
  - metagenomics
  - table
  - combining
  - merging
tools:
  - krakentools:
      description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
      homepage: https://github.com/jenniferlu717/KrakenTools
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - kreports:
      type: file
      description: List of kraken-style report files
      pattern: "*.{txt,kreport}"

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 kreport file of all input files
      pattern: "*.txt"

authors:
  - "@jfy133"