mem/time setting updates; sex params

TitanCNA.snakefile

@@ -45,7 +45,7 @@ rule runTitanCNA:
 		numCores=config["TitanCNA_numCores"],
 		normal=config["TitanCNA_normalInit"],
 		chrs=config["TitanCNA_chrs"],
-		gender=config["gender"],
+		sex=config["sex"],
 		estimatePloidy=config["TitanCNA_estimatePloidy"],
 		estimateClonality=config["TitanCNA_estimateClonality"],
 		estimateNormal=config["TitanCNA_estimateNormal"],
@@ -58,11 +58,11 @@ rule runTitanCNA:
 		plotYlim=config["TitanCNA_plotYlim"],
 		mem=config["TitanCNA_mem"],
 		runtime=config["TitanCNA_runtime"],
-		pe=config["TitanCNA_numCores"]
+		pe=config["TitanCNA_pe"]
 	log:
 		"logs/titan/titanCNA_ploidy{ploidy}/{tumor}_cluster{clustNum}.log"
 	shell:
-		"Rscript {params.titanRscript} --id {wildcards.tumor} --hetFile {input.alleleCounts} --cnFile {input.corrDepth} --numClusters {wildcards.clustNum} --numCores {params.numCores} --normal_0 {params.normal} --ploidy_0 {wildcards.ploidy} --chrs \"{params.chrs}\" --gender {params.gender} --haplotypeBinSize {params.haplotypeBinSize} --estimateNormal {params.estimateNormal} --estimatePloidy {params.estimatePloidy} --estimateClonality {params.estimateClonality}  --centromere {params.centromere} --genomeBuild {params.genomeBuild} --genomeStyle {params.genomeStyle} --libdir {params.libdir} --alphaK {params.alphaK} --alphaR {params.alphaR} --alleleModel Gaussian --txnExpLen {params.txnExpLen} --plotYlim \"{params.plotYlim}\" --cytobandFile {params.cytobandFile} --outFile {output.titan} --outSeg {output.segTxt} --outParam {output.param} --outIGV {output.seg} --outPlotDir {output.outRoot} > {log} 2> {log}"
+		"Rscript {params.titanRscript} --id {wildcards.tumor} --hetFile {input.alleleCounts} --cnFile {input.corrDepth} --numClusters {wildcards.clustNum} --numCores {params.numCores} --normal_0 {params.normal} --ploidy_0 {wildcards.ploidy} --chrs \"{params.chrs}\" --sex {params.sex} --haplotypeBinSize {params.haplotypeBinSize} --estimateNormal {params.estimateNormal} --estimatePloidy {params.estimatePloidy} --estimateClonality {params.estimateClonality}  --centromere {params.centromere} --genomeBuild {params.genomeBuild} --genomeStyle {params.genomeStyle} --libdir {params.libdir} --alphaK {params.alphaK} --alphaR {params.alphaR} --alleleModel Gaussian --txnExpLen {params.txnExpLen} --plotYlim \"{params.plotYlim}\" --cytobandFile {params.cytobandFile} --outFile {output.titan} --outSeg {output.segTxt} --outParam {output.param} --outIGV {output.seg} --outPlotDir {output.outRoot} > {log} 2> {log}"
 
 
 rule combineTitanAndIchorCNA:
@@ -80,14 +80,14 @@ rule combineTitanAndIchorCNA:
 		combineScript=config["TitanCNA_combineTitanIchorCNA"],
 		libdir=config["TitanCNA_libdir"],
 		centromere=config["centromere"],
-		gender=config["gender"],
+		sex=config["sex"],
 		mem=config["std_mem"],
 		runtime=config["std_runtime"],
 		pe=config["std_numCores"]
 	log:
 		"logs/titan/titanCNA_ploidy{ploidy}/{tumor}_cluster{clustNum}.combineTitanIchorCNA.log"
 	shell:
-		"Rscript {params.combineScript} --libdir {params.libdir} --titanSeg {input.titanSeg} --titanBin {input.titanBin} --titanParam {input.titanParam} --ichorSeg {input.ichorSeg} --ichorBin {input.ichorBin} --ichorParam {input.ichorParam} --gender {params.gender} --outSegFile {output.segFile} --outBinFile {output.binFile} --centromere {params.centromere} > {log} 2> {log}"	
+		"Rscript {params.combineScript} --libdir {params.libdir} --titanSeg {input.titanSeg} --titanBin {input.titanBin} --titanParam {input.titanParam} --ichorSeg {input.ichorSeg} --ichorBin {input.ichorBin} --ichorParam {input.ichorParam} --sex {params.sex} --outSegFile {output.segFile} --outBinFile {output.binFile} --centromere {params.centromere} > {log} 2> {log}"	
 
 
 rule selectSolution:

code/combineTITAN-ichor.R

@@ -19,7 +19,7 @@ option_list <- list(
   	make_option(c("--ichorSeg"), type="character", help="ichorCNA segs.txt file. Required."),
 	make_option(c("--ichorBin"), type="character", help="ichorCNA cna.seg file. Required."),
 	make_option(c("--ichorParams"), type="character", help="ichorCNA params.txt file. Required."),
-	make_option(c("--gender"), type="character", default="female", help="female or male. Default [%default]."),
+	make_option(c("--sex"), type="character", default="female", help="female or male. Default [%default]."),
 	make_option(c("--libdir"), type="character", help="TitanCNA directory path to source R files if custom changes made."),
   	make_option(c("--outSegFile"), type="character", help="New combined segment file. Required"),
   	make_option(c("--outBinFile"), type="character", help="New combined bin-level file. Required"),
@@ -36,7 +36,7 @@ titanParams <- opt$titanParams
 ichorSeg <- opt$ichorSeg
 ichorBin <- opt$ichorBin
 ichorParams <- opt$ichorParams
-gender <- opt$gender
+gender <- opt$sex
 outSegFile <- opt$outSegFile
 outBinFile <- opt$outBinFile
 centromere <- opt$centromere

code/titanCNA_v1.15.0_TenX.R

@@ -34,7 +34,7 @@ option_list <- list(
 	make_option(c("--genomeStyle"), type = "character", default = "NCBI", help = "NCBI or UCSC chromosome naming convention; use UCSC if desired output is to have \"chr\" string. [Default: %default]"),
 	make_option(c("--genomeBuild"), type = "character", default = "hg38", help="Genome build to use; will load Seqinfo from GenomeInfoDb."),
 	make_option(c("--chrs"), type = "character", default = "c(1:22, 'X')", help = "Chromosomes to analyze; string [Default: %default"),
-	make_option(c("--gender"), type = "character", default = "male", help = "User specified gender: male or female [Default: %default]"),
+	make_option(c("--sex"), type = "character", default = "male", help = "User specified sex: male or female [Default: %default]"),
 	make_option(c("--cytobandFile"), type = "character", default = NULL, help = "Cytoband file should be provided only if reference genome is hg38."),
 	make_option(c("--mapWig"), type = "character", default = NULL, help = "Mappability score file for bin sizes matching cnfile. [Default: %default]"),
 	make_option(c("--mapThres"), type = "numeric", default = 0.9, help = "Minimum mappability score threshold to use; float [Default: %default]"),
@@ -100,7 +100,7 @@ chrs <- eval(parse(text = opt$chrs))
 genomeStyle <- opt$genomeStyle
 genomeBuild <- opt$genomeBuild
 cytobandFile <- opt$cytobandFile
-gender <- opt$gender
+sex <- opt$sex
 mapWig <- opt$mapWig
 centromere <- opt$centromere
 haplotypeBinSize <- opt$haplotypeBinSize
@@ -144,8 +144,8 @@ outImage <- gsub(".titan.txt", ".RData", outfile)
 ## set up chromosome naming convention ##
 seqinfo <- Seqinfo(genome=genomeBuild)
 seqlevelsStyle(chrs) <- genomeStyle
-## exclude chrX if gender==male ##
-if (gender == "male" || gender == "Male" || gender == "MALE"){
+## exclude chrX if sex==male ##
+if (sex == "male" || sex == "Male" || sex == "MALE"){
 	chrs <- chrs[!grepl("X", chrs)]
 }
 
@@ -222,7 +222,7 @@ save.image(file=outImage)
 #### OUTPUT SEGMENTS ####
 segs <- outputTitanSegments(results, id, convergeParams, filename = NULL, igvfilename = outigv)
 corrIntCN.results <- correctIntegerCN(results, segs, 1 - norm, ploidy, maxCNtoCorrect.autosomes = maxCN, 
-		maxCNtoCorrect.X = NULL, minPurityToCorrect = 0.2, gender = gender, chrs = chrs)
+		maxCNtoCorrect.X = NULL, minPurityToCorrect = 0.2, gender = sex, chrs = chrs)
 results <- corrIntCN.results$cn
 segs <- corrIntCN.results$segs
 message("Writing results to ", outfile, ",\n\t", outseg, ",\n\t", outparam)
@@ -240,7 +240,7 @@ if (genomeBuild == "hg38" && file.exists(cytobandFile)){
 	#cytoband$V1 <- setGenomeStyle(cytoband$V1, genomeStyle = genomeStyle)
 }
 
-if (gender == "male"){
+if (sex == "male"){
 	chrsToPlot <- chrs[!grepl("X", chrs)]
 }else{
 	chrsToPlot <- chrs

config/config.yaml

@@ -9,7 +9,7 @@ phaseCounts_counts_script:  code/getTumourAlleleCountsAtHETSites.py
 TitanCNA_rscript: code/titanCNA_v1.15.0_TenX.R
 TitanCNA_selectSolutionRscript: code/selectSolution.R
 TitanCNA_combineTitanIchorCNA:  code/combineTITAN-ichor.R
-TitanCNA_libdir:  /path/to/TitahCNA/ ## optional
+TitanCNA_libdir:  /path/to/TitanCNA/ ## optional
 ichorCNA_libdir:  /path/to/ichorCNA/ ## optional
 
 ## reference settings ##
@@ -18,7 +18,7 @@ genomeStyle:  UCSC
 snpVCF:  /path/to/hapmap_3.3.hg38.vcf.gz ## optional
 cytobandFile:  data/cytoBand_hg38.txt # only need if hg38
 centromere:  data/GRCh38.GCA_000001405.2_centromere_acen.txt
-gender:  male
+sex:  male
 
 ## LongRanger params ##
 bamFileName:  phased_possorted_bam.bam
@@ -56,7 +56,7 @@ het_minBaseQuality:  10
 het_minMapQuality:  20
 
 ## TitanCNA params ##
-TitanCNA_maxNumClonalClusters: 1
+TitanCNA_maxNumClonalClusters: 2
 TitanCNA_chrs:  c(1:22, \"X\")
 TitanCNA_normalInit:  0.5
 TitanCNA_maxPloidy:  3
@@ -69,9 +69,10 @@ TitanCNA_alphaR:  5000
 TitanCNA_txnExpLen: 1e15
 TitanCNA_plotYlim:  c(-2,4)
 TitanCNA_solutionThreshold: 0.05
+TitanCNA_numCores:  1
 TitanCNA_mem:  16G
-TitanCNA_runtime:  "10:00:00"
-TitanCNA_numCores: -pe smp 1 -binding linear:1  
+TitanCNA_runtime:  "300:00:00"
+TitanCNA_pe: -pe smp 1 -binding linear:1  
 
 
 

getPhasedAlleleCounts.snakefile

@@ -10,9 +10,8 @@ def getLRFullPath(base, filename):
 
 rule phasedCounts:
 	input: 
-		expand("results/phasedCounts/tumCounts/{tumor}/{tumor}.tumCounts.{chr}.txt", tumor=config["pairings"], chr=CHRS),		
 		expand("results/phasedCounts/tumCounts/{tumor}.tumCounts.txt", tumor=config["pairings"])
-
+		
 rule getHETsites:
 	input:
 		lambda wildcards: getLRFullPath(config["samples"][config["pairings"][wildcards.tumor]], config["phaseVariantFileName"])
@@ -33,7 +32,7 @@ rule getHETsites:
 	log:
 		"logs/phasedCounts/hetPosns/{tumor}.phasedHETsites.log"
 	shell:
-		"Rscript {params.getHETsitesScript} --inVCF {input} --genomeBuild {params.genomeBuild} --genomeStyle {params.genomeStyle} --snpDB {params.snpDB} --minQuality {params.minQual} --minDepth {params.minDepth} --minVAF {params.minVAF} --altCountField AD --libdir {params.libdir} --outVCF {output} 2> {log}"
+		"Rscript {params.getHETsitesScript} --inVCF {input} --genomeBuild {params.genomeBuild} --genomeStyle {params.genomeStyle} --snpDB {params.snpDB} --minQuality {params.minQual} --minDepth {params.minDepth} --minVAF {params.minVAF} --altCountField AD --libdir {params.libdir} --outVCF {output} > {log} 2> {log}"
 
 
 rule getAlleleCountsByChr:

moleculeCoverage.snakefile

@@ -34,7 +34,7 @@ rule bxTile:
 		bxTools=config["bxTools"],
 		samTools=config["samTools"],
 		mapQual=config["bx_mapQual"],
-		bedFile=config["bx_bedFileRoot"]
+		bedFile=config["bx_bedFileRoot"],
 		mem=config["std_mem"],
 		runtime=config["std_runtime"],
 		pe=config["std_numCores"]