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
      licence: ["MIT"]
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"
