name: hmmcopy_readcounter
description: readCounter function from HMMcopy utilities, used to generate read in windows
keywords:
  - hmmcopy
  - readcounter
  - cnv
tools:
  - hmmcopy:
      description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
      homepage: https://github.com/shahcompbio/hmmcopy_utils
      documentation: https://github.com/shahcompbio/hmmcopy_utils
      tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
      doi: ""
      licence: ['GPL v3']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - wig:
      type: file
      description: A wig file with the number of reads lying within each window in each chromosome
      pattern: "*.wig"

authors:
  - "@sppearce"