name: bedtools_slop
description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
keywords:
    - bed
    - slopBed
tools:
    - bedtools:
        description: |
            A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
        documentation: https://bedtools.readthedocs.io/en/latest/
        
params:
    - l:
        type: integer
        description:
            The number of base pairs to subtract from the start coordinate
    - r:
        type: integer
        description:
        The number of base pairs to add to the end coordinate
    - 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

input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bed:
        type: file
        description: List of bed files
        pattern: "*.{bed}"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bed:
        type: file
        description: Edited bed file
        pattern: "*.{slopbed}"

    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"