From cd4a8f4c2b6bc01674a8255f3441a4c7c4271251 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 8 Feb 2016 11:14:37 +0100
Subject: [PATCH] Fix merge file
---
.../main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
index cff40a548..89b608407 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
@@ -75,7 +75,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
}
}
- override def keepMergedFiles: Boolean = config("keep_merged_files", default = false)
+ override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner)
override def summarySettings = super.summarySettings + ("use_indel_realigner" -> useIndelRealigner)
--
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