name: homer_groseq
description: Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.
keywords:
  - homer
  - groseq
  - nascent
modules:
  - homer/maketagdirectory
  - homer/makeucscfile
  - homer/findpeaks
  - homer/pos2bed
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - input:
      type: list
      description: list of BAM files, also able to take SAM and BED as input
      pattern: "[ *.{bam/sam/bed} ]"
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
output:
  - tagdir:
      type: directory
      description: The "Tag Directory"
      pattern: "*_tagdir"
  - bedGraph:
      type: file
      description: The UCSC bed graph
      pattern: "*.bedGraph.gz"
  - peaks:
      type: file
      description: The found peaks
      pattern: "*.peaks.txt"
  - bed:
      type: file
      description: A BED file of the found peaks
      pattern: "*.bed"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@Emiller88"
