From 8acebe9adb834eb838221a8774bc180308ce6383 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Dec 2015 13:31:38 +0100
Subject: [PATCH] Fixed double flexiprep
---
.../scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index cdb0a034f..02f35d7c5 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -74,7 +74,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
}
protected def executeFlexiprep(r1: File, r2: Option[File]): (File, Option[File]) = {
- if (config("skip_flexiprep", default = false)) {
+ if (!config("skip_flexiprep", default = false).asBoolean) {
val flexiprep = new Flexiprep(this)
flexiprep.input_R1 = r1
flexiprep.input_R2 = r2
--
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