name: qualimap_bamqc
description: Evaluate alignment data
keywords:
    - quality control
    - qc
    - bam
tools:
    - qualimap:
        description: |
          Qualimap 2 is a platform-independent application written in
          Java and R that provides both a Graphical User Interface and
          a command-line interface to facilitate the quality control of
          alignment sequencing data and its derivatives like feature counts.
        homepage: http://qualimap.bioinfo.cipf.es/
        documentation: http://qualimap.conesalab.org/doc_html/index.html
        doi: 10.1093/bioinformatics/bts503
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 ]
    - bam:
        type: file
        description: BAM file
        pattern: "*.{bam}"
    - gff:
        type: file
        description: Feature file with regions of interest
        pattern: "*.{gff,gtf,bed}"
    - use_gff:
        type: boolean
        description: Specifies if feature file should be used or not
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - results:
        type: dir
        description: Qualimap results dir
        pattern: "*/*"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@phue"