name: controlfreec_assesssignificance
description: Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC
keywords:
  - cna
  - cnv
  - somatic
  - single
  - tumor-only
tools:
  - controlfreec/assesssignificance:
      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 ]
  - cnvs:
      type: file
      description: _CNVs file generated by FREEC
      pattern: "*._CNVs"
  - ratio:
      type: file
      description: ratio file generated by FREEC
      pattern: "*.ratio.txt"

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"
  - p_value_txt:
      type: file
      description: CNV file containing p_values for each call
      pattern: "*.p.value.txt"

authors:
  - "@FriederikeHanssen"