name: bedtools_bamtobed
description: Converts a bam file to a bed12 file.
keywords:
  - bam
  - 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/complement.html
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Input BAM file
      pattern: "*.{bam}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: Bed file containing genomic intervals.
      pattern: "*.{bed}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@yuukiiwa"
  - "@drpatelh"