Fix output folders

vizapp/server.R

@@ -64,18 +64,18 @@ shinyServer(
             n = length(cancer.list) + 1
             for(i in cancer.list){
               incProgress(1/n, detail = paste0("collating data ", count, " of ", length(cancer.list)))
-              if(!file.exists(paste0("../Expression/out_genes/",gene,"/",i,".txt"))){
+              if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",i,".txt"))){
                 cat("File not present\n")
-                if(!dir.exists(paste0("../Expression/out_genes/",gene))){
-                  system(paste0("mkdir ../Expression/out_genes/",gene))
+                if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+                  system(paste0("mkdir ../output/Expression/out_genes/",gene))
                   cat("Made directory\n")
                 }
-                system(paste0("ls ../Expression/*",i,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
-                              gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+                system(paste0("ls ../output/Expression/*",i,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../output/Expression/out_genes/",
+                              gene,"/","$fname; grep -wi ",gene," $line >> ../output/Expression/out_genes/",gene,"/","$fname;done"))
                 cat("creating data\n")
                 
               }
-              temp <- as.data.frame(t(read.table(paste("../Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
+              temp <- as.data.frame(t(read.table(paste("../output/Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
               temp$type <- as.factor(ifelse(grepl("11",row.names(temp)),"Normal","Tumor"))
               temp$cancer <- rep(i,nrow(temp))
               if(ncol(temp)<3 | length(unique(temp$type))<2){
@@ -125,22 +125,22 @@ shinyServer(
             incProgress(1/n, detail = "Getting expression data")
             #Import Expression and Clinical Data
             cat(paste0("going to read expression ",cancer,"\n"))
-            if(!file.exists(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"))){
+            if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"))){
               cat("File not present\n")
-              if(!dir.exists(paste0("../Expression/out_genes/",gene))){
-                system(paste0("mkdir ../Expression/out_genes/",gene))
+              if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+                system(paste0("mkdir ../output/Expression/out_genes/",gene))
                 cat("Made directory\n")
               }
-              system(paste0("ls ../Expression/*",cancer,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
-                            gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+              system(paste0("ls ../output/Expression/*",cancer,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../output/Expression/out_genes/",
+                            gene,"/","$fname; grep -wi ",gene," $line >> ../output/Expression/out_genes/",gene,"/","$fname;done"))
               cat("creating data\n")
               
             }
-            exp <- read.table(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F) 
-            #exp <- read.table(paste0("../Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
+            exp <- read.table(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F) 
+            #exp <- read.table(paste0("../output/Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
             cat("going to read clinical data\n")
             incProgress(1/n, detail = "Getting clinical data")
-            clinical <- read.table(paste("../Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
+            clinical <- read.table(paste("../output/Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
             
             
             #Process Clinical
@@ -291,18 +291,18 @@ shinyServer(
           n = length(cancer.list) + 1
           for(i in cancer.list){
             #incProgress(1/n, detail = paste0("collating data ", count, " of ", length(cancer.list)))
-            if(!file.exists(paste0("../Expression/out_genes/",gene,"/",i,".txt"))){
+            if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",i,".txt"))){
               cat("File not present\n")
-              if(!dir.exists(paste0("../Expression/out_genes/",gene))){
-                system(paste0("mkdir ../Expression/out_genes/",gene))
+              if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+                system(paste0("mkdir ../output/Expression/out_genes/",gene))
                 cat("Made directory\n")
               }
-              system(paste0("ls ../Expression/*",i,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
-                            gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+              system(paste0("ls ../output/Expression/*",i,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../output/Expression/out_genes/",
+                            gene,"/","$fname; grep -wi ",gene," $line >> ../output/Expression/out_genes/",gene,"/","$fname;done"))
               cat("creating data\n")
               
             }
-            temp <- as.data.frame(t(read.table(paste("../Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
+            temp <- as.data.frame(t(read.table(paste("../output/Expression/out_genes/",gene,"/",i,".txt",sep=""),header=T,sep="\t",row.names=1)))
             temp$type <- as.factor(ifelse(grepl("11",row.names(temp)),"Normal","Tumor"))
             temp$cancer <- rep(i,nrow(temp))
             if(ncol(temp)<3 | length(unique(temp$type))<2){
@@ -352,22 +352,22 @@ shinyServer(
           #incProgress(1/n, detail = "Getting expression data")
           #Import Expression and Clinical Data
           cat(paste0("going to read expression ",cancer,"\n"))
-          if(!file.exists(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"))){
+          if(!file.exists(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"))){
             cat("File not present\n")
-            if(!dir.exists(paste0("../Expression/out_genes/",gene))){
-              system(paste0("mkdir ../Expression/out_genes/",gene))
+            if(!dir.exists(paste0("../output/Expression/out_genes/",gene))){
+              system(paste0("mkdir ../output/Expression/out_genes/",gene))
               cat("Made directory\n")
             }
-            system(paste0("ls ../Expression/*",cancer,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../Expression/out_genes/",
-                          gene,"/","$fname; grep -wi ",gene," $line >> ../Expression/out_genes/",gene,"/","$fname;done"))
+            system(paste0("ls ../output/Expression/*",cancer,"*txt | while read line ; do fname=$(basename $line); head -1 $line > ../output/Expression/out_genes/",
+                          gene,"/","$fname; grep -wi ",gene," $line >> ../output/Expression/out_genes/",gene,"/","$fname;done"))
             cat("creating data\n")
             
           }
-          exp <- read.table(paste0("../Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F) 
-          #exp <- read.table(paste0("../Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
+          exp <- read.table(paste0("../output/Expression/out_genes/",gene,"/",cancer,".txt"),header=T,row.names=1,check.names=F) 
+          #exp <- read.table(paste0("../output/Expression/",cancer,".txt"),header=T,row.names=1,check.names=F) #Instead of importing entire expression matrix should import single gene.
           cat("going to read clinical data\n")
           #incProgress(1/n, detail = "Getting clinical data")
-          clinical <- read.table(paste("../Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
+          clinical <- read.table(paste("../output/Clinical/",cancer,".txt",sep=""),header=T,row.names=1,sep="\t")
           
           
           #Process Clinical

vizapp/ui.R

@@ -6,15 +6,15 @@ shinyUI(
         selectInput("operation","Select Plot Type",choices = c("Boxplot","Survival")),
         conditionalPanel(condition = "input.operation=='Boxplot'",
                          selectInput("cancerType","Select one or more cancer types",
-                                     choices = substr(list.files("../Expression/",pattern=".txt"),1,
-                                                      nchar(list.files("../Expression/",pattern=".txt"))-4),
+                                     choices = substr(list.files("../output/Expression/",pattern=".txt"),1,
+                                                      nchar(list.files("../output/Expression/",pattern=".txt"))-4),
                                      multiple = TRUE),
                          textInput("gene","Please input one gene of interest",placeholder = "Gene name ie TRIM21")
         ),
         conditionalPanel(condition="input.operation=='Survival'",
                          selectInput("cancerType2","Select a cancer type",
-                                     choices = substr(list.files("../Expression/",pattern=".txt"),1,
-                                                      nchar(list.files("../Expression/",pattern=".txt"))-4)),
+                                     choices = substr(list.files("../output/Expression/",pattern=".txt"),1,
+                                                      nchar(list.files("../output/Expression/",pattern=".txt"))-4)),
                          textInput("gene2","Please input one gene of interest",placeholder = "Gene name ie BRCA1"),
                          selectInput("operation2","Select automatic or manual cutoff", choices = c("Automatic", "Manual"))
                          

workflow/main.nf

@@ -8,7 +8,7 @@ params.run = "TRUE"
 
 process copy {
 
-  publishDir "$baseDir/../", mode: 'copy'
+  publishDir "$baseDir/../output/", mode: 'copy'
 
   input: