name: cnvpytor_callcnvs
description: command line tool for calling CNVs in whole genome sequencing data
  - CNV calling
tools:
  - cnvpytor:
      description: calling CNVs using read depth
      homepage: https://github.com/abyzovlab/CNVpytor
      documentation: https://github.com/abyzovlab/CNVpytor
      tool_dev_url: https://github.com/abyzovlab/CNVpytor
      doi: "10.1101/2021.01.27.428472v1"
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - pytor:
      type: file
      description: pytor file containing partitions of read depth histograms using mean-shift method
      pattern: "*.{pytor}"
  - bin_sizes:
      type: string
      description: list of binsizes separated by space e.g. "1000 10000" and "1000"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - pytor:
      type: file
      description: pytor files containing cnv calls
      pattern: "*.{pytor}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@sima-r"