From aef401d49e495c4bd920865c111bb2456384e9e1 Mon Sep 17 00:00:00 2001
From: rhpvorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 11 May 2017 15:42:42 +0200
Subject: [PATCH] Add fix to increase default fastqc memory to 4 GB per core,
to make single-threaded runs easier.
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index bd20abc40..a2362a8a6 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -51,6 +51,8 @@ class Fastqc(val parent: Configurable) extends BiopetCommandLineFunction with Ve
def versionCommand = executable + " --version"
override def defaultThreads = 4
+ override def defaultCoreMemory: Double = 4.0
+
/** Sets contaminants and adapters when not yet set */
override def beforeGraph() {
this.jobOutputFile = new File(output.getParentFile, s".${fastqfile.getName}.fastqc.out")
--
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