name: seqkit_split2
description: Split single or paired-end fastq.gz files
keywords:
    - split
    - fastq
tools:
    - seqkit:
        description: |
            Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
        homepage: https://github.com/shenwei356/seqkit
        documentation: https://bioinf.shenwei.me/seqkit/
        doi: 10.1371/journal.pone.0163962
params:
    - outdir:
        type: string
        description: |
            The pipeline's output directory. By default, the module will
            output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
        type: string
        description: |
            Value for the Nextflow `publishDir` mode parameter.
            Available: symlink, rellink, link, copy, copyNoFollow, move.
    - enable_conda:
        type: boolean
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
    - singularity_pull_docker_container:
        type: boolean
        description: |
            Instead of directly downloading Singularity images for use with Singularity,
            force the workflow to pull and convert Docker containers instead.
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - reads:
        type: file
        description: FastQ files
        pattern: "*.{fq.gz/fastq.gz}"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - reads:
        type: file
        description: Split fastq files
        pattern: "*.{fq.gz/fastq.gz}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@FriederikeHanssen"