enable users to specify sex

For now, assumes that sample set contains all males or all females but not both. #72 For sample sets with both, please use `male` so that chrX is excluded allelic CN analysis
gavinha · May 7, 2019 · 5aa0249 · 5aa0249
1 parent ea4cdd6
commit 5aa0249
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/scripts/snakemake/TitanCNA.snakefile b/scripts/snakemake/TitanCNA.snakefile
@@ -38,6 +38,7 @@ rule runTitanCNA:
 		numCores=config["TitanCNA_numCores"],
 		normal=config["TitanCNA_normalInit"],
 		chrs=config["TitanCNA_chrs"],
+		sex=config["sex"],
 		genomeStyle=config["genomeStyle"],
 		genomeBuild=config["genomeBuild"],
 		cytobandFile=config["cytobandFile"],
@@ -53,7 +54,7 @@ rule runTitanCNA:
 	log:
 		"logs/titan/hmm/titanCNA_ploidy{ploidy}/{tumor}_cluster{clustNum}.log"
 	shell:
-		"Rscript {params.titanRscript} --hetFile {input.alleleCounts} --cnFile {input.corrDepth} --outFile {output.titan} --outSeg {output.segTxt} --outParam {output.param} --outIGV {output.seg} --outPlotDir {params.outRoot} --libdir {params.libdir} --id {wildcards.tumor} --numClusters {wildcards.clustNum} --numCores {params.numCores} --normal_0 {params.normal} --ploidy_0 {wildcards.ploidy} --genomeStyle {params.genomeStyle} --genomeBuild {params.genomeBuild} --cytobandFile {params.cytobandFile} --chrs \"{params.chrs}\" --estimateNormal {params.estimateNormal} --estimatePloidy {params.estimatePloidy} --estimateClonality {params.estimateClonality}  --centromere {params.centromere} --alphaK {params.alphaK} --txnExpLen {params.txnExpLen} --plotYlim \"{params.plotYlim}\" > {log} 2> {log}"
+		"Rscript {params.titanRscript} --hetFile {input.alleleCounts} --cnFile {input.corrDepth} --outFile {output.titan} --outSeg {output.segTxt} --outParam {output.param} --outIGV {output.seg} --outPlotDir {params.outRoot} --libdir {params.libdir} --id {wildcards.tumor} --numClusters {wildcards.clustNum} --numCores {params.numCores} --normal_0 {params.normal} --ploidy_0 {wildcards.ploidy} --genomeStyle {params.genomeStyle} --genomeBuild {params.genomeBuild} --cytobandFile {params.cytobandFile} --chrs \"{params.chrs}\" --gender {params.sex} --estimateNormal {params.estimateNormal} --estimatePloidy {params.estimatePloidy} --estimateClonality {params.estimateClonality}  --centromere {params.centromere} --alphaK {params.alphaK} --txnExpLen {params.txnExpLen} --plotYlim \"{params.plotYlim}\" > {log} 2> {log}"
 
 #--alleleModel {params.alleleModel} --alphaR {params.alphaR}