name: "pear"
description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger.
keywords:
  - pair-end
  - read
  - merge
tools:
  - "pear":
      description: "paired-end read merger"
      homepage: "https://cme.h-its.org/exelixis/web/software/pear/"
      documentation: "https://cme.h-its.org/exelixis/web/software/pear/doc.html"
      licence: "['Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - reads:
      type: file
      description: |
        List of input FastQ files with paired-end reads forward and reverse.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - assembled:
      type: file
      description: FastQ file containing Assembled reads.
      pattern: "*.{fastq.gz}"
  - unassembled:
      type: file
      description: FastQ files containing Unassembled forward and reverse reads.
      pattern: "*.{fastq.gz}"
  - discarded:
      type: file
      description: FastQ file containing discarded reads.
      pattern: "*.{fastq.gz}"

authors:
  - "@mirpedrol"
