diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
similarity index 93%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
rename to biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
index 1c08a4f6811331433e375b633f36ab95943fd9b6..905b56f32f2e96ef7356cecff25526c0470038f4 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.wrappers.aligners
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
@@ -9,7 +9,7 @@ import scala.sys.process._
 class Bwa(val globalConfig: Config) extends CommandLineFunction {
   def this() = this(new Config(Map()))
   this.analysisName = "bwa"
-  val config: Config = globalConfig.getAsConfig("bwa")
+  val config: Config = Config.mergeConfigs(globalConfig.getAsConfig("bwa"), globalConfig)
   logger.debug("Config for " + this.analysisName + ": " + config)
 
   @Argument(doc="Bwa executeble", shortName="bwa_exe", required=false) var bwa_exe: String = config.getAsString("exe", "/usr/local/bin/bwa")
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
similarity index 97%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
rename to biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
index 6580013f8a7ff4d9d418aabdb992b0da842d7825..0cca136cb39b72119864e5df97972879094fe165 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.wrappers.aligners
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction