name: bedtools_sort
description: Sorts a feature file by chromosome and other criteria.
keywords:
  - bed
  - sort
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/sort.html
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - intervals:
      type: file
      description: BED/BEDGRAPH
      pattern: "*.{bed|bedGraph}"

  - extension:
      type: string
      description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - sorted:
      type: file
      description: Sorted output file
      pattern: "*.${extension}"

  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@Emiller88"
  - "@sruthipsuresh"
  - "@drpatelh"
  - "@chris-cheshire"
