Lint R scripts

workflow/apps/r/addShiftVals.R

@@ -10,25 +10,25 @@ library(sos)
 args <- commandArgs(TRUE)
 
 if (length(args) >= 1) {
-  finalTable <- args[1]
+  finalTable <- file.path(args[1])
 } else {
   finalTable <- "REMcRdy_lm_only.csv-finalTable.csv"  # for legacy workflow
 }
 
 if (length(args) >= 2) {
-  shiftFile <- args[2]
+  shiftFile <- file.path(args[2])
 } else {
   shiftFile <- "Shift_only.csv"  # for legacy workflow
 }
 
 if (length(args) >= 3) {
-  studyInfo <- args[3]
+  studyInfo <- file.path(args[3])
 } else {
   studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow
 }
 
 if (length(args) >= 4) {
-  output <- args[4]
+  output <- file.path(args[4])
 } else {
   output <- "REMcHeatmaps/REMcWithShift.csv" # for legacy workflow
 }