name: cat_fastq
description: Concatenates fastq files
keywords:
    - fastq
    - concatenate
tools:
    - cat:
        description: |
            The cat utility reads files sequentially, writing them to the standard output.
        documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
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:
    input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - reads:
        type: list
        description: |
            List of input FastQ files to be concatenated.
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - reads:
        type: file
        description: Merged fastq file
        pattern: "*.{merged.fastq.gz}"
authors:
    - "@joseespinosa"
    - "@drpatelh"