name: bedtools_merge
description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
keywords:
    - bed
    - merge
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/content/tools/merge.html
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bed:
        type: file
        description: Input BED file
        pattern: "*.{bed}"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bed:
        type: file
        description: Overlapped bed file with combined features
        pattern: "*.{bed}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@Emiller88"
    - "@sruthipsuresh"
    - "@drpatelh"