name: bedtools_subtract
description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
keywords:
    - bed
    - gff
    - vcf
    - subtract
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/subtract.html

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - intervals1:
      type: file
      description: BED/GFF/VCF
      pattern: "*.{bed|gff|vcf}"
  - intervals2:
      type: file
      description: BED/GFF/VCF
      pattern: "*.{bed|gff|vcf}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: File containing the difference between the two sets of features
      patters: "*.bed"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@sidorov-si"