name: bedtools_map
description: Allows one to screen for overlaps between two sets of genomic features.
keywords:
  - bed
  - vcf
  - gff
  - map
  - bedtools
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/map.html
      licence: ["MIT"]
      identifier: biotools:bedtools
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - intervals1:
        type: file
        description: BAM/BED/GFF/VCF
        pattern: "*.{bed|gff|vcf}"
    - intervals2:
        type: file
        description: BAM/BED/GFF/VCF
        pattern: "*.{bed|gff|vcf}"
  - - meta2:
        type: map
        description: |
          Groovy Map containing reference chromosome sizes
          e.g. [ id:'test' ]
    - chrom_sizes:
        type: file
        description: Chromosome sizes file
        pattern: "*{.sizes,.txt}"
output:
  - mapped:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.${extension}":
          type: file
          description: File containing the description of overlaps found between the features
            in A and the features in B, with statistics
          pattern: "*.${extension}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@ekushele"
maintainers:
  - "@ekushele"
