From 108358038a6f53133369941bd86e3ae68aa506be Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 19 Jan 2016 13:41:34 +0100
Subject: [PATCH] Raise default memory for varscan
---
.../sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
index 9dc5b91a8..085b1bc37 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
@@ -39,6 +39,8 @@ class VarscanMpileup2cns(val root: Configurable) extends Varscan {
var vcfSampleList: Option[File] = config("vcf_sample_list")
var variants: Option[Int] = config("variants")
+ override def defaultCoreMemory = 6.0
+
override def beforeGraph(): Unit = {
val validValues: Set[Int] = Set(0, 1)
// check for boolean vars that are passed as ints
--
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