diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 92ea25fc98265435cdac9a86de9a07fb97de5d61..caa014a1e3012e7b3ebc43f05ea5729350c28122 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -73,9 +73,10 @@ class Config(var map: Map[String, Any]) extends Logging {
   var defaultCache: Map[ConfigValueIndex, ConfigValue] = Map()
 
   def contains(s: String): Boolean = map.contains(s)
-  def contains(requestedIndex: ConfigValueIndex): Boolean = contains(requestedIndex.module, requestedIndex.path, requestedIndex.key)
-  def contains(module: String, path: List[String], key: String): Boolean = {
-    val requestedIndex = ConfigValueIndex(module, path, key)
+  def contains(requestedIndex: ConfigValueIndex, freeVar:Boolean): Boolean = contains(requestedIndex.module, requestedIndex.path, requestedIndex.key, freeVar)
+  def contains(requestedIndex: ConfigValueIndex): Boolean = contains(requestedIndex.module, requestedIndex.path, requestedIndex.key, true)
+  def contains(module: String, path: List[String], key: String, freeVar:Boolean = true): Boolean = {
+    val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
     if (notFoundCache.contains(requestedIndex)) return false
     else if (foundCache.contains(requestedIndex)) return true
     else {
@@ -89,12 +90,13 @@ class Config(var map: Map[String, Any]) extends Logging {
             foundCache += (requestedIndex -> ConfigValue.apply(requestedIndex, ConfigValueIndex(module, submodules2, key), p(key)))
             return true
           }
-
-          val p2 = getMapFromPath(submodules2)
-          //logger.debug("p2: " + p2)
-          if (p2.contains(key)) {
-            foundCache += (requestedIndex -> ConfigValue.apply(requestedIndex, ConfigValueIndex(module, submodules2, key), p2(key)))
-            return true
+          if (freeVar) {
+            val p2 = getMapFromPath(submodules2)
+            //logger.debug("p2: " + p2)
+            if (p2.contains(key)) {
+              foundCache += (requestedIndex -> ConfigValue.apply(requestedIndex, ConfigValueIndex(module, submodules2, key), p2(key)))
+              return true
+            }
           }
           submodules2 = submodules2.init
         }
@@ -104,7 +106,7 @@ class Config(var map: Map[String, Any]) extends Logging {
       if (p.contains(key)) { // Module is not nested
         foundCache += (requestedIndex -> ConfigValue.apply(requestedIndex, ConfigValueIndex(module, Nil, key), p(key)))
         return true
-      } else if (this.contains(key)) { // Root value of json
+      } else if (this.contains(key) && freeVar) { // Root value of json
         foundCache += (requestedIndex -> ConfigValue.apply(requestedIndex, ConfigValueIndex("", Nil, key), get(key)))
         return true
       } else { // At this point key is not found on the path
@@ -117,24 +119,27 @@ class Config(var map: Map[String, Any]) extends Logging {
   private def get(key: String): Any = map(key)
   private def get(key: String, default: Any): Any = if (contains(key)) get(key) else default
 
-  def apply(module: String, path: List[String], key: String, default: Any): ConfigValue = {
+  def apply(module: String, path: List[String], key: String, default: Any = null, freeVar:Boolean = true): ConfigValue = {
     val requestedIndex = ConfigValueIndex(module, path, key)
-    if (contains(requestedIndex)) return foundCache(requestedIndex)
-    else {
+    if (contains(requestedIndex, freeVar)) return foundCache(requestedIndex)
+    else if (default != null) {
       defaultCache += (requestedIndex -> ConfigValue.apply(requestedIndex, null, default, true))
       return defaultCache(requestedIndex)
-    }
-  }
-
-  def apply(module: String, path: List[String], key: String): ConfigValue = {
-    val requestedIndex = ConfigValueIndex(module, path, key)
-    if (contains(requestedIndex)) return foundCache(requestedIndex)
-    else {
+    } else {
       logger.error("Value in config could not be found but it seems required, index: " + requestedIndex)
       throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
     }
   }
 
+//  def apply(module: String, path: List[String], key: String, freeVar:Boolean = true): ConfigValue = {
+//    val requestedIndex = ConfigValueIndex(module, path, key)
+//    if (contains(requestedIndex, freeVar)) return foundCache(requestedIndex)
+//    else {
+//      logger.error("Value in config could not be found but it seems required, index: " + requestedIndex)
+//      throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
+//    }
+//  }
+
   private def getMapFromPath(path: List[String]): Map[String, Any] = {
     var returnMap: Map[String, Any] = map
     for (m <- path) {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala
index fadf6bae6ac2fb077e88b95f4d23ea59cfe93231..4d515b347d9522d62facfa9c53dea7d43e27e5a0 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala
@@ -1,14 +1,14 @@
 package nl.lumc.sasc.biopet.core.config
 
-class ConfigValueIndex(val module: String, val path: List[String], val key: String) {
-  override def toString = "Module = " + module + ", path = " + path + ", key = " + key
+class ConfigValueIndex(val module: String, val path: List[String], val key: String, val freeVar:Boolean = true) {
+  override def toString = "Module = " + module + ",  path = " + path + ",  key = " + key + ",  freeVar = " + freeVar
 }
 
 object ConfigValueIndex {
   private var cache: Map[(String, List[String], String), ConfigValueIndex] = Map()
 
-  def apply(module: String, path: List[String], key: String): ConfigValueIndex = {
-    if (!cache.contains(module, path, key)) cache += ((module, path, key) -> new ConfigValueIndex(module, path, key))
+  def apply(module: String, path: List[String], key: String, freeVar:Boolean = true): ConfigValueIndex = {
+    if (!cache.contains(module, path, key)) cache += ((module, path, key) -> new ConfigValueIndex(module, path, key, freeVar))
     return cache(module, path, key)
   }
 }
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index 01d1e55e1378b815f8fbf7d82a10aa4a59b58f31..750a560afda25cb3f526869d26ba0d749a962037 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -10,27 +10,27 @@ trait Configurable extends Logging {
   protected val configName = getClass.getSimpleName.toLowerCase
   protected val configFullPath = configName :: configPath
 
-  def config(key: String, default: Any = null, submodule: String = null, required: Boolean = false): ConfigValue = {
+  def config(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar:Boolean = true): ConfigValue = {
     val m = if (submodule != null) submodule else configName
     val p = if (submodule != null) configName :: configPath else configPath
-    if (!configContains(key, submodule) && default == null) {
+    if (!configContains(key, submodule, freeVar) && default == null) {
       if (required) {
         logger.error("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
         throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
       } else return null
     }
-    if (default == null) return globalConfig(m, p, key)
-    else return globalConfig(m, p, key, default)
+    if (default == null) return globalConfig(m, p, key, freeVar)
+    else return globalConfig(m, p, key, default, freeVar)
   }
   //def config(key:String, default:Any) = globalConfig(configName, configPath, key, default)
   //def config(key:String, default:Any, module:String) = globalConfig(module, configName :: configPath, key, default)
 
   //def configContains(key:String) = globalConfig.contains(configName, configPath, key)
-  def configContains(key: String, submodule: String = null) = {
+  def configContains(key: String, submodule: String = null, freeVar:Boolean = true) = {
     val m = if (submodule != null) submodule else configName
     val p = if (submodule != null) configName :: configPath else configPath
 
-    globalConfig.contains(m, p, key)
+    globalConfig.contains(m, p, key, freeVar)
   }
 
   implicit def configValue2file(value: ConfigValue): File = if (value != null) new File(Configurable.any2string(value.value)) else null
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 2755877a632641b9fe3a2a70f097aefb99d0a78e..b40c2b25a2c74862a518b14509d9515f65b3dfcb 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -19,7 +19,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   var output: File = _
 
   executable = config("exe", default = "fastqc")
-  var java_exe: String = config("exe", default = "java", submodule = "java")
+  var java_exe: String = config("exe", default = "java", submodule = "java", freeVar = false)
   var kmers: Option[Int] = config("kmers")
   var quiet: Boolean = config("quiet")
   var noextract: Boolean = config("noextract")