update the pipeline where it crashes

SCRIPTS/DE/clusterHeatmap.R

@@ -15,7 +15,11 @@ option_list = list(
         make_option(c("-a", "--sampleAbstract"), type="character", default=NULL, 
               help="sample abstract file path", metavar="character"),
 	make_option(c("-o", "--outdir"), type="character", default=".", 
-              help="output directory [default= %default]", metavar="character")
+              help="output directory [default= %default]", metavar="character"),
+	make_option(c("--ignore-plate-effect"), dest="ignore_plate_effect", action="store_true", default=FALSE, 
+              help="Ignore plate effect if multiplate design [default= %default]"),
+	make_option(c("--ignore-batch-effect"), dest="ignore_batch_effect", action="store_true", default=FALSE, 
+              help="Ignore batch effect [default= %default]")
 ); 
 
 opt_parser = OptionParser(option_list=option_list);
@@ -86,9 +90,9 @@ nboot=30  #if bootsrap, number of bootstrap replications
 sampleAnnot<-lire(sampleTable)
 
 # If column named "batchEffect" exists, apply batch correction
-batchEffect<-FALSE; if(batchEffectCol %in% colnames(sampleAnnot)) batchEffect<-TRUE
+batchEffect<-FALSE; if((!opt$ignore_batch_effect) && (batchEffectCol %in% colnames(sampleAnnot))) batchEffect<-TRUE
 # If column named "plateBatch" exists, apply batch correction
-plateBatch<-FALSE; if(plateBatchCol %in% colnames(sampleAnnot)) plateBatch<-TRUE
+plateBatch<-FALSE; if((!opt$ignore_plate_effect) && (plateBatchCol %in% colnames(sampleAnnot))) plateBatch<-TRUE
 
 if(batchEffect || plateBatch){
         exprDatT=lire(paste(outputDir,"/exprTransformedAdjusted.tsv",sep=""))

SCRIPTS/DE/normalization.R

@@ -16,9 +16,7 @@ option_list = list(
 	make_option(c("--ignore-plate-effect"), dest="ignore_plate_effect", action="store_true", default=FALSE, 
               help="Ignore plate effect if multiplate design [default= %default]"),
 	make_option(c("--ignore-batch-effect"), dest="ignore_batch_effect", action="store_true", default=FALSE, 
-              help="Ignore batch effect [default= %default]"),
-	make_option(c("--ignore-all-factors"), dest="ignore_factors", action="store_true", default=FALSE, 
-              help="Ignore all factors [default= %default]")
+              help="Ignore batch effect [default= %default]")
 ); 
 
 opt_parser = OptionParser(option_list=option_list);
@@ -53,9 +51,9 @@ exprDat<-lire(expressionData)
 sampleAnnot<-lire(sampleTable)
 
 # If column named "batchEffect" exists, apply batch correction
-batchEffect<-FALSE; if((!(opt$ignore_factors || opt$ignore_batch_effect)) && (batchEffectCol %in% colnames(sampleAnnot))) batchEffect<-TRUE
+batchEffect<-FALSE; if((!opt$ignore_batch_effect) && (batchEffectCol %in% colnames(sampleAnnot))) batchEffect<-TRUE
 # If column named "plateBatch" exists, apply batch correction
-plateBatch<-FALSE; if((!(opt$ignore_factors || opt$ignore_plate_effect)) && (plateBatchCol %in% colnames(sampleAnnot))) plateBatch<-TRUE
+plateBatch<-FALSE; if((!opt$ignore_plate_effect) && (plateBatchCol %in% colnames(sampleAnnot))) plateBatch<-TRUE
 
 sampleAnnot[,condCol]<-as.factor(as.character(sampleAnnot[,condCol]))
 exprDat<-exprDat[,c(rownames(sampleAnnot))]

SCRIPTS/DE/qualityControl.R

@@ -11,7 +11,11 @@ option_list = list(
 	make_option(c("-s", "--sampleTable"), type="character", default=NULL, 
               help="sample table file path", metavar="character"),
 	make_option(c("-o", "--outdir"), type="character", default=".", 
-              help="output directory [default= %default]", metavar="character")
+              help="output directory [default= %default]", metavar="character"),
+	make_option(c("--ignore-plate-effect"), dest="ignore_plate_effect", action="store_true", default=FALSE, 
+              help="Ignore plate effect if multiplate design [default= %default]"),
+	make_option(c("--ignore-batch-effect"), dest="ignore_batch_effect", action="store_true", default=FALSE, 
+              help="Ignore batch effect [default= %default]")
 ); 
 
 opt_parser = OptionParser(option_list=option_list);
@@ -156,9 +160,9 @@ sampleAnnot<-lire(sampleTable)
 
 
 # If column named "batchEffect" exists, apply batch correction
-batchEffect<-FALSE; if(batchEffectCol %in% colnames(sampleAnnot)) batchEffect<-TRUE
+batchEffect<-FALSE; if((!opt$ignore_batch_effect) && (batchEffectCol %in% colnames(sampleAnnot))) batchEffect<-TRUE
 # If column named "plateBatch" exists, apply batch correction
-plateBatch<-FALSE; if(plateBatchCol %in% colnames(sampleAnnot)) plateBatch<-TRUE
+plateBatch<-FALSE; if((!opt$ignore_plate_effect) && (plateBatchCol %in% colnames(sampleAnnot))) plateBatch<-TRUE
 
 acpT<-ACP(exprDatT)
 compo=length(which(acpT$percentVar>0.05))+1

SCRIPTS/common.smk

@@ -107,10 +107,11 @@ rule deClusterHeatmap:
 		MAINDIR+"/{project}/"+config["de_folder"]+"/HeatmapCorPearson.png",
 		MAINDIR+"/{project}/"+config["de_folder"]+"/heatmap.RData"
 	params:
-		outdir = MAINDIR+"/{project}/"+config["de_folder"]
+		outdir = MAINDIR+"/{project}/"+config["de_folder"],
+		additional_params = lambda wildcards: config["comparisons"][wildcards.project].get("normalizationOptions", [])
 	shell:
 		"""
-		Rscript {wfbasedir}/SCRIPTS/DE/clusterHeatmap.R -e {input.expressionTable} -s {input.sampleTable} -a {input.sampleAbstract} -o {params.outdir}
+		Rscript {wfbasedir}/SCRIPTS/DE/clusterHeatmap.R -e {input.expressionTable} -s {input.sampleTable} -a {input.sampleAbstract} -o {params.outdir} {params.additional_params}
 		"""
 
 rule deQualityControls:
@@ -120,10 +121,11 @@ rule deQualityControls:
 	output:
 		MAINDIR+"/{project}/"+config["de_folder"]+"/PCA.png"
 	params:
-		outdir = MAINDIR+"/{project}/"+config["de_folder"]
+		outdir = MAINDIR+"/{project}/"+config["de_folder"],
+		additional_params = lambda wildcards: config["comparisons"][wildcards.project].get("normalizationOptions", [])
 	shell:
 		"""
-		Rscript {wfbasedir}/SCRIPTS/DE/qualityControl.R -e {input.expressionTable} -s {input.sampleTable} -o {params.outdir}
+		Rscript {wfbasedir}/SCRIPTS/DE/qualityControl.R -e {input.expressionTable} -s {input.sampleTable} -o {params.outdir} {params.additional_params}
 		"""
 
 rule deNormalization: