name: bedtools_merge
description: combines overlapping or “book-ended” features in an interval file into
  a single feature which spans all of the combined features.
keywords:
  - bed
  - merge
  - bedtools
  - overlapped bed
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/merge.html
      licence: ["MIT"]
      identifier: biotools:bedtools
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}"
output:
  - bed:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.bed":
          type: file
          description: Overlapped bed file with combined features
          pattern: "*.{bed}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@edmundmiller"
  - "@sruthipsuresh"
  - "@drpatelh"
maintainers:
  - "@edmundmiller"
  - "@sruthipsuresh"
  - "@drpatelh"
