From c2fdfed68304f7d05aadaea4cabcbadaf0bcd5fa Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 9 Aug 2016 22:28:19 +0200
Subject: [PATCH] Force no flexiprep in gears

---
 .../lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
index 1e9586913..9aefe7eca 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
@@ -67,6 +67,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
 
   override def defaults = super.defaults ++ Map("reordersam" -> Map("allow_incomplete_dict_concordance" -> true))
 
+  override def fixedValues = Map("gearssingle" -> Map("skip_flexiprep" -> true))
+
   /** In a default multisample mapping run there are no multsample jobs. This method can be overriden by other pipelines */
   def addMultiSampleJobs(): Unit = {
     // this code will be executed after all code of all samples is executed
-- 
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