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"