name: bedtools_genomecov
description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
keywords:
    - bed
    - bam
    - genomecov
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/genomecov.html
        licence: ['MIT']
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - intervals:
        type: file
        description: BAM/BED/GFF/VCF
        pattern: "*.{bam|bed|gff|vcf}"
    - scale:
        type: value
        description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
    - sizes:
        type: file
        description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
    - extension:
        type: string
        description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - genomecov:
        type: file
        description: Computed genome coverage file
        pattern: "*.${extension}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@Emiller88"
    - "@sruthipsuresh"
    - "@drpatelh"
    - "@sidorov-si"
    - "@chris-cheshire"