name: bedtools_complement
description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
keywords:
    - bed
    - complement
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/complement.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}"
    - sizes:
        type: file
        description: File which defines the chromosome lengths for a given genome
        pattern: "*.{sizes}"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bed:
        type: file
        description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
        pattern: "*.{bed}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@Emiller88"
    - "@sruthipsuresh"
    - "@drpatelh"