change to heredoc

mergecounts.wdl

@@ -3,15 +3,27 @@ task MergeCounts {
     String outputFile
     String idVar
     String measurementVar
-    File script
 
-    command {
-        Rscript ${script} \
-        ${idVar} \
-        ${measurementVar} \
-        ${sep=" " inputFiles} \
-        > ${outputFile}
-    }
+    # Based on a script by Szymon Kielbasa/Ioannis Moustakas
+    command <<<
+        R --no-save --slave <<CODE > ${outputFile}
+            library(dplyr)
+            library(reshape2)
+
+            listOfFiles <- c("${sep='", "' inputFiles}")
+
+            d <- do.call(rbind, lapply(listOfFiles, function(file){
+                d <- read.table(file, header=TRUE, comment.char="#")
+                colI <- grep(${measurementVar}, colnames(d))
+                colnames(d)[colI] <- strsplit(file, "/")[[1]][3]
+                d <- d %>% melt(id.vars=${idVar}, measure.vars=colI,
+                    variable.name="sample", value.name="count")
+            }))
+
+            d <- d %>% dcast(paste0(${idVar}, " ~ sample"), value.var="count")
+            write.table(d, sep="\t", quote=FALSE, row.names=FALSE)
+        CODE
+    >>>
 
     output {
         File mergedCounts = outputFile

scripts/merge_counts.R

-# Author: Ioannis Moustakas, i.moustakas@lumc.nl (Based on a script by Szymon Kielbasa)
-# Modified by: Davy Cats, d.cats@lumc.nl
-# Title: Merge count files from featureCouns output
-# Use: Rscript merge_counts.R columnIDToMergeOn columnIDBeingMerged listOfFilesToBeMerged... > outputFile
-
-### Load Packages
-library(dplyr)
-library(reshape2)
-
-### load arguments from the command line
-args <- commandArgs(trailingOnly=TRUE)
-idVars <- args[1]
-measureVars <- args[2]
-listOfFiles <- args[3:length(args)]
-
-### Iterate over the list of files that are being merged and
-### change the column name to the sample name
-d <- do.call(rbind, lapply(listOfFiles, function(file){
-    d <- read.table(file, header=TRUE, comment.char="#")
-    colI <- grep(measureVars, colnames(d))
-    colnames(d)[colI] <- strsplit(file, "/")[[1]][3]
-    d <- d %>% melt(id.vars=idVars, measure.vars=colI,
-                    variable.name="sample", value.name="count")
-}))
-
-### Reformat the data frame and output (in STDOUT) the merged table.
-d <- d %>% dcast(paste0(idVars, " ~ sample"), value.var="count")
-write.table(d, sep="\t", quote=FALSE, row.names=FALSE)