name: bedtools_makewindows

description: Makes adjacent or sliding windows across a genome or BED file.
keywords:
  - bed
  - windows
tools:
  - bedtools:
      description: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
      homepage: https://bedtools.readthedocs.io
      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
      tool_dev_url: None
      doi: "10.1093/bioinformatics/btq033"
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - regions:
      type: file
      description: BED file OR Genome details file (<chromName><TAB><chromSize>)
      pattern: "*.{bed,fai,tab}"
  - use_bed:
      type: boolean
      description: true = input is a BED file; false = input is a genome details file
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - tab:
      type: file
      description: Windows TAB file (BED or BED-like format)
      pattern: "*.tab"
authors:
  - "@kevbrick"