Fix RScript input

workflow/apps/r/PairwiseLK.R

@@ -19,7 +19,7 @@ args <- commandArgs(TRUE)
 exp_name <- args[1]
 exp_name2 <- args[2]
 
-if (length(args) > 3) {
+if (length(args) >= 3) {
   study_info_file  <- args[3]
 } else {
   study_info_file  <- "StudyInfo.csv" 

workflow/apps/r/addShiftVals.R

@@ -9,25 +9,25 @@ library(sos)
 
 args=commandArgs(TRUE)
 
-if (length(args) > 1) {
+if (length(args) >= 1) {
   finalTable <- args[1]
 } else {
   finalTable <- "REMcRdy_lm_only.csv-finalTable.csv"  # for legacy workflow
 }
 
-if (length(args) > 2) {
+if (length(args) >= 2) {
   shiftFile <- args[2]
 } else {
   shiftFile <- "Shift_only.csv"  # for legacy workflow
 }
 
-if (length(args) > 3) {
+if (length(args) >= 3) {
   studyInfo <- args[3]
 } else {
   studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow
 }
 
-if (length(args) > 4) {
+if (length(args) >= 4) {
   output <- args[4]
 } else {
   output<- "REMcHeatmaps/REMcWithShift.csv" # for legacy workflow

workflow/apps/r/createHeatMaps.R

@@ -8,13 +8,13 @@ library(gplots)
 args <- commandArgs(TRUE)
 
 # Set output dir
-if (length(args) > 1) {
+if (length(args) >= 1) {
   input_finalTable <- args[1]
 } else {
   input_finalTable <- "/REMcHeatmaps/REMcWithShift.csv" # for legacy workflow
 }
 
-if (length(args) > 2) {
+if (length(args) >= 2) {
   outDir <- args[2]
 } else {
   outDir <- "/REMcHeatmaps/REMcWithShift.csv" # for legacy workflow

workflow/apps/r/gtaTemplate.R

@@ -16,25 +16,25 @@ args <- commandArgs(TRUE)
 
 exp_name <- args[1]
 
-if (length(args) > 2) {
+if (length(args) >= 2) {
   zscores_file <- args[2]
 } else {
   zscores_file <- "zscores/zscores_interaction.csv" # https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
 }
 
-if (length(args) > 3) {
+if (length(args) >= 3) {
   sgd_terms_file <- args[3]
 } else {
   sgd_terms_file <- "go_terms.tab"
 }
 
-if (length(args) > 4) {
+if (length(args) >= 4) {
   sgd_features_file <- args[4]
 } else {
   sgd_features_file <- "gene_association.sgd" # https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
 }
 
-if (length(args) > 5) {
+if (length(args) >= 5) {
   output_dir <- args[5]
 } else {
   output_dir <- "../../out/gta" # https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd

workflow/apps/r/interactions.R

@@ -26,28 +26,28 @@ args <- commandArgs(TRUE)
 inputFile <- args[1]
 
 # Set output dir
-if (length(args) > 2) {
+if (length(args) >= 2) {
   outDir <- args[2]
 } else {
   outDir <- "/ZScores/" # for legacy workflow
 }
 
 # Set StudyInfo file path
-if (length(args) > 3) {
+if (length(args) >= 3) {
   studyInfo <- args[3]
 } else {
   studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow
 }
 
 # Set SGDgeneList file path
-if (length(args) > 4) {
+if (length(args) >= 4) {
   SGDgeneList <- args[4]
 } else {
   SGDgeneList <- "../Code/SGD_features.tab" # for legacy workflow
 }
 
 # Set standard deviation
-if (length(args) > 5) {
+if (length(args) >= 5) {
   delBGFactor <- args[5]
 } else {
   # User prompt for std multiplier Value
@@ -78,11 +78,9 @@ expNumber <- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3] <- delBGFactor
 write.csv(Labels,file=studyInfo,row.names = FALSE)
 
-###############################################################################
+# BEGIN USER DATA SELECTION SECTION
-################### BEGIN USER DATA SELECTION SECTION #########################
-###############################################################################
 
-#read in the data
+# Read in the data
 X <- read.delim(inputFile,skip=2,as.is=T,row.names=1,strip.white=TRUE)
 X <- X[!(X[[1]]%in%c("","Scan")),]
 #X <- X[!(X[[1]]%in%c(61:76)),]  #Remove dAmp plates which are Scans 61 thru 76

workflow/apps/r/joinInteractExps.R

@@ -8,14 +8,14 @@ library(dplyr)
 args <- commandArgs(TRUE)
 
 # Set output dir
-if (length(args) > 1) {
+if (length(args) >= 1) {
   outDir <- args[1]
 } else {
   outDir <- "./" # for legacy workflow
 }
 
 # Set sd value
-if (length(args) > 2) {
+if (length(args) >= 2) {
   sd <- args[2]
 } else {
   sd <- 2 # default value
@@ -23,7 +23,7 @@ if (length(args) > 2) {
 print(paste("SD=",sd))
 
 # Set studyInfo file
-if (length(args) > 3) {
+if (length(args) >= 3) {
   studyInfo <- args[3]
 } else {
   studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow

workflow/qhtcp-workflow

@@ -1334,7 +1334,7 @@ qhtcp() {
       "$STUDY_INFO_FILE" \
       "$STUDY_DIR/zscores/" \
       "$APPS_DIR/r/SGD_features.tab" \
-      5
+      3
   done
 
   # Run remc as part of the QHTCP process