name: "kat_hist"
description: Creates a histogram of the number of distinct k-mers having a given frequency.
keywords:
  - k-mer
  - histogram
  - count
tools:
  - "kat":
      description: "KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts"
      homepage: https://www.earlham.ac.uk/kat-tools
      documentation: https://kat.readthedocs.io/en/latest/index.html
      tool_dev_url: https://github.com/TGAC/KAT
      doi: http://bioinformatics.oxfordjournals.org/content/early/2016/10/20/bioinformatics.btw663.abstract
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.

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"
  - hist:
      type: file
      description: KAT histogram of k-mer counts
      pattern: "*.hist"
  - json:
      type: file
      description: KAT histogram summary of distance analysis
      pattern: "*.hist.dist_analysis.json"
  - png:
      type: file
      description: KAT plot of k-mer histogram in PNG format
      pattern: "*.png"
  - ps:
      type: file
      description: KAT plot of k-mer histogram in PS format
      pattern: "*.ps"
  - pdf:
      type: file
      description: KAT plot of k-mer histogram in PDF format
      pattern: "*.pdf"
  - jellyfish_hash:
      type: file
      description: Jellyfish hash file
      pattern: "*-hist.jf*"

authors:
  - "@mahesh-panchal"