name: homer_annotatepeaks
description: Annotate peaks with HOMER suite
keywords:
  - annotations
  - peaks
  - bed
tools:
  - homer:
      description: |
        HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
      documentation: http://homer.ucsd.edu/homer/
      doi: 10.1016/j.molcel.2010.05.004.
      licence: ["GPL-3.0-or-later"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - peaks:
      type: file
      description: The peak files in bed format
      pattern: "*.bed"
  - fasta:
      type: file
      description: Fasta file of reference genome
      pattern: "*.fasta"
  - gtf:
      type: file
      description: GTF file of reference genome
      pattern: "*.gtf"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - annotated_peaks:
      type: file
      description: The annotated peaks
      pattern: "*annotatePeaks.txt"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@kevinmenden"