From b6b2b73ed31e2fa023b92adc9414083f79d435df Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 20 Mar 2018 10:09:45 +0100
Subject: [PATCH] change to heredoc
---
mergecounts.wdl | 28 ++++++++++++++++++++--------
scripts/merge_counts.R | 28 ----------------------------
2 files changed, 20 insertions(+), 36 deletions(-)
delete mode 100644 scripts/merge_counts.R
diff --git a/mergecounts.wdl b/mergecounts.wdl
index c71247d..de4bee4 100644
--- a/mergecounts.wdl
+++ b/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
diff --git a/scripts/merge_counts.R b/scripts/merge_counts.R
deleted file mode 100644
index 8963994..0000000
--- a/scripts/merge_counts.R
+++ /dev/null
@@ -1,28 +0,0 @@
-# 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)
--
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