name: controlfreec description: Copy number and genotype annotation from whole genome and whole exome sequencing data 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: - args: type: map description: | Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. `sex = meta.sex`: For default values, please check the documentation above. ``` { [ "general" :[ "bedgraphoutput": (optional), "breakpointthreshold": (optional), "breakpointtype": (optional), "coefficientofvariation": (optional), "contamination": (optional), "contaminationadjustment": (optional), "degree": (optional), "forcegccontentnormalization": (optional), "gccontentprofile": (optional), "intercept": (optional), "mincnalength": (optional), "minmappabilityperwindow": (optional), "minexpectedgc": (optional), "maxexpectedgc": (optional), "minimalsubclonepresence": (optional), "noisydata": (optional), "ploidy": (optional), "printNA": (optional), "readcountthreshold": (optional), "sex": (optional), "step": (optional), "telocentromeric": (optional), "uniquematch": (optional), "window": (optional) ], "control":[ "inputformat": (required), "mateorientation": (optional), ], "sample":[ "inputformat": (required), "mateorientation": (optional), ], "BAF":[ "minimalcoverageperposition": (optional), "minimalqualityperposition": (optional), "shiftinquality": (optional) ] ] } ``` - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - mateFile_normal: type: file description: File with mapped reads pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - mateFile_tumor: type: file description: File with mapped reads pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - cpn_normal: type: file description: Raw copy number profiles (optional) pattern: "*.cpn" - cpn_tumor: type: file description: Raw copy number profiles (optional) pattern: "*.cpn" - minipileup_normal: type: file description: miniPileup file from previous run (optional) pattern: "*.pileup" - minipileup_tumor: type: file description: miniPileup file from previous run (optional) pattern: "*.pileup" - fasta: type: file description: Reference file (optional; required if args 'makePileup' is set) pattern: "*.{fasta,fna,fa}" - fai: type: file description: Fasta index pattern: "*.fai" - snp_position: type: file description: pattern: "*.{}" - known_snps: type: file description: File with known SNPs pattern: "*.{vcf,vcf.gz}" - known_snps_tbi: type: file description: Index of known_snps pattern: "*.tbi" - chr_directory: type: file description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided) pattern: "*/" - mappability: type: file description: Contains information of mappable positions (optional) pattern: "*.gem" - target_bed: type: file description: Sorted bed file containing capture regions (optional) pattern: "*.bed" 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" - bedgraph: type: file description: Bedgraph format for the UCSC genome browser pattern: ".bedgraph" - control_cpn: type: file description: files with raw copy number profiles pattern: "*_control.cpn" - sample_cpn: type: file description: files with raw copy number profiles pattern: "*_sample.cpn" - gcprofile_cpn: type: file description: file with GC-content profile. pattern: "GC_profile.*.cpn" - BAF: type: file description: file B-allele frequencies for each possibly heterozygous SNP position pattern: "*_BAF.txt" - CNV: type: file description: file with coordinates of predicted copy number alterations. pattern: "*_CNVs" - info: type: file description: parsable file with information about FREEC run pattern: "*_info.txt" - ratio: type: file description: file with ratios and predicted copy number alterations for each window pattern: "*_ratio.txt" - config: type: file description: Config file used to run Control-FREEC pattern: "config.txt" authors: - "@FriederikeHanssen"