From 6b7aaacf1cbaeec042d14f17f7d7afe1ca14baf6 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <sajvanderzeeuw@sasc-sander.lumcnet.prod.intern>
Date: Thu, 6 Nov 2014 15:41:21 +0100
Subject: [PATCH] Changes made to alter the number of GC cores
---
.../scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index 398393f98..43ab44f4e 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -6,6 +6,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
class SamToFastq(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.SamToFastq"
+ javaGCThreads = config("gcthreads", default = 2)
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: File = _
--
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