name: flash
description: Perform merging of mate paired-end sequencing reads
keywords:
  - sort
  - reads merging
  - merge mate pairs
tools:
  - flash:
      description: |
        Merge mates from fragments that are shorter than twice the read length
      homepage: https://ccb.jhu.edu/software/FLASH/
      documentation: {}
      doi: 10.1093/bioinformatics/btr507
      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 2; i.e., paired-end data.
      pattern: "*fastq.gz"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: The merged fastq reads
      pattern: "*fastq.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@Erkison"