name: MultiQC
description: Aggregate results from bioinformatics analyses across many samples into a single report
keywords:
    - QC
    - bioinformatics tools
    - Beautiful stand-alone HTML report
tools:
    - multiqc:
        description: |
            MultiQC searches a given directory for analysis logs and compiles a HTML report.
            It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
        homepage: https://multiqc.info/
        documentation: https://multiqc.info/docs/
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:
    - multiqc_files:
        type: file
        description: |
            List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
output:
    - report:
        type: file
        description: MultiQC report file
        pattern: "multiqc_report.html"
    - data:
        type: dir
        description: MultiQC data dir
        pattern: "multiqc_data"
    - plots:
        type: file
        description: Plots created by MultiQC
        pattern: "*_data"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@abhi18av"
    - "@bunop"
    - "@drpatelh"