From 08c1fa5505da2089a4a68c20962367661448e18e Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 24 May 2018 14:29:44 +0200
Subject: [PATCH] fix mergeCounts
---
mergecounts.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/mergecounts.wdl b/mergecounts.wdl
index 8aa2a92..75d5123 100644
--- a/mergecounts.wdl
+++ b/mergecounts.wdl
@@ -12,7 +12,7 @@ task MergeCounts {
set -e -o pipefail
mkdir -p ${sub(outputFile, basename(outputFile) + "$", "")}
${preCommand}
- R --no-save --slave <<CODE > ${outputFile}
+ R --no-save --slave <<CODE
library(dplyr)
library(reshape2)
@@ -23,7 +23,7 @@ task MergeCounts {
header <- ${true="TRUE" false="FALSE" inputHasHeader}
d <- do.call(rbind, lapply(listOfFiles, function(file){
- d <- read.table(file, header=header, comment.char="#")
+ d <- read.table(file, sep="\t", header=header, comment.char="#")
splitPath <- strsplit(file, "/")[[1]]
colnames(d)[valueI] <- sub("\\\.[^\\\.]*$", "",
@@ -34,7 +34,7 @@ task MergeCounts {
}))
d <- d %>% dcast(feature ~ sample, value.var="count")
- write.table(d, sep="\t", quote=FALSE, row.names=FALSE)
+ write.table(d, file="${outputFile}", sep="\t", quote=FALSE, row.names=FALSE)
CODE
>>>
--
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