name: seqtk_mergepe
description: Interleave pair-end reads from FastQ files
keywords:
  - interleave
tools:
  - seqtk:
      description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
      homepage: https://github.com/lh3/seqtk
      documentation:  https://docs.csc.fi/apps/seqtk/
      tool_dev_url: https://github.com/lh3/seqtk
      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 FastQ files of size 1 and 2 for single-end and paired-end data,respectively.
      pattern: "*.{fastq.gz}"

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: If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair.
      pattern: "*.{fastq.gz}"

authors:
  - "@emnilsson"