name: controlfreec_makegraph 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"