name: seqkit_pair
description: match up paired-end reads from two fastq files
keywords:
  - seqkit
  - pair
tools:
  - seqkit:
      description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
      homepage: https://bioinf.shenwei.me/seqkit/usage/
      documentation: https://bioinf.shenwei.me/seqkit/usage/
      tool_dev_url: https://github.com/shenwei356/seqkit/
      doi: "10.1371/journal.pone.0163962"
      licence: ["MIT"]

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

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"
  - reads:
      type: file
      description: Paired fastq reads
      pattern: "*.paired.fastq.gz"
  - unpaired_reads:
      type: file
      description: Unpaired reads (optional)
      pattern: "*.unpaired.fastq.gz"

authors:
  - "@sateeshperi"
  - "@mjcipriano"
  - "@hseabolt"