name: controlfreec_makegraph2
description: Plot Freec output
keywords:
  - cna
  - cnv
  - somatic
  - single
  - tumor-only
tools:
  - controlfreec:
      description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
      homepage: http://boevalab.inf.ethz.ch/FREEC
      documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
      tool_dev_url: https://github.com/BoevaLab/FREEC/
      doi: "10.1093/bioinformatics/btq635"
      licence: ["GPL >=2"]

input:
  # Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - ratio:
      type: file
      description: ratio file generated by FREEC
      pattern: "*.ratio.txt"
  - baf:
      type: file
      description: .BAF file generated by FREEC
      pattern: "*.BAF"

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"
  - png_baf:
      type: file
      description: Image of BAF plot
      pattern: "*_BAF.png"
  - png_ratio_log2:
      type: file
      description: Image of ratio log2 plot
      pattern: "*_ratio.log2.png"
  - png_ratio:
      type: file
      description: Image of ratio plot
      pattern: "*_ratio.png"

authors:
  - "@FriederikeHanssen"
