From bfd2bddb0f1cd0de0e3c3178ee8677fb36a3666b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 14 Nov 2014 16:39:01 +0100
Subject: [PATCH] Add gatk jar option
---
.../scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
index 44e5e62fe..54280581f 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
@@ -6,6 +6,8 @@ import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
memoryLimit = Option(3)
+ if (config.contains("gatk_jar")) jarFile = config("gatk_jar")
+
override val defaultVmem = "7G"
if (config.contains("intervals", submodule = "gatk")) intervals = config("intervals", submodule = "gatk").getFileList
--
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