Fix for BIOPET-398

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -41,8 +41,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   @Argument(required = false)
   var outputName: String = _
 
-  lazy val krakenScript = if (config("gears_use_kraken", default = true)) Some(new GearsKraken(this)) else None
-  lazy val centrifugeScript = if (config("gears_use_centrifuge", default = false)) Some(new GearsCentrifuge(this)) else None
+  lazy val krakenScript = if (config("gears_use_kraken", default = false)) Some(new GearsKraken(this)) else None
+  lazy val centrifugeScript = if (config("gears_use_centrifuge", default = true)) Some(new GearsCentrifuge(this)) else None
   lazy val qiimeRatx = if (config("gears_use_qiime_rtax", default = false)) Some(new GearsQiimeRtax(this)) else None
   lazy val qiimeClosed = if (config("gears_use_qiime_closed", default = false)) Some(new GearsQiimeClosed(this)) else None
   lazy val qiimeOpen = if (config("gears_use_qiime_open", default = false)) Some(new GearsQiimeOpen(this)) else None