From 379c84747891f43d33dec6dbd4c9b024070b0409 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 May 2014 09:33:56 +0200
Subject: [PATCH] - Fixed Bwa on Gatk, did called the wrong config
---
.../src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index 389e118b8..9beec1e93 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -186,7 +186,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
flexiprep.script
addAll(flexiprep.functions) // Add function of flexiprep to curent function pool
- val bwaCommand = new Bwa(config.getAsConfig("bwa"))
+ val bwaCommand = new Bwa(config)
bwaCommand.R1 = flexiprep.outputFiles("output_R1")
if (paired) bwaCommand.R2 = flexiprep.outputFiles("output_R2")
bwaCommand.referenceFile = referenceFile
--
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