From a5d6318760da851fc7fb813aa3064b3a7c73b34d Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 4 Apr 2018 13:39:40 +0200
Subject: [PATCH] add memory settings to extractAdapters
---
fastqc.wdl | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index 515e9a6..d14faf9 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -65,7 +65,7 @@ task extractAdapters {
command {
set -e
mkdir -p ${outputDir}
- java -jar ${extractAdaptersFastqcJar} \
+ java -Xmx3G -jar ${extractAdaptersFastqcJar} \
--inputFile ${inputFile} \
${"--adapterOutputFile " + adapterOutputFilePath } \
${"--contamsOutputFile " + contamsOutputFilePath } \
@@ -82,6 +82,10 @@ task extractAdapters {
Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
}
+
+ runtime {
+ memory: 6
+ }
}
task getConfiguration {
--
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