name: bbmap_clumpify
description: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates
keywords:
  - clumping fastqs
  - smaller fastqs
  - deduping
  - fastq
tools:
  - bbmap:
      description: BBMap is a short read aligner, as well as various other bioinformatic tools.
      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/
      documentation: https://www.biostars.org/p/225338/
      tool_dev_url: None
      doi: ""
      licence: ["UC-LBL license (see package)"]

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 ]
  - reads:
      type: file
      description: The reordered/clumped (and if necessary deduped) fastq reads
      pattern: "*.clumped.fastq.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - log:
      type: file
      description: Clumpify log file
      pattern: "*clumpify.log"

authors:
  - "@tamuanand"