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"]
      identifier: ""

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:
  - png_baf:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_BAF.png":
          type: file
          description: Image of BAF plot
          pattern: "*_BAF.png"
  - png_ratio_log2:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_ratio.log2.png":
          type: file
          description: Image of ratio log2 plot
          pattern: "*_ratio.log2.png"
  - png_ratio:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*_ratio.png":
          type: file
          description: Image of ratio plot
          pattern: "*_ratio.png"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@FriederikeHanssen"
