Removed required argument for config, now handled by conversions, not a option means required

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

@@ -133,11 +133,12 @@ class Config(var map: Map[String, Any]) extends Logging {
    */
   protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
     val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
-    if (contains(requestedIndex)) return foundCache(requestedIndex)
+    if (contains(requestedIndex)) foundCache(requestedIndex)
     else if (default != null) {
       defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
-      return defaultCache(requestedIndex)
-    } else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
+      defaultCache(requestedIndex)
+    } else ConfigValue(requestedIndex, null, null, freeVar)
+    //else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
   }
 
   def writeReport(id: String, directory: String): Unit = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

@@ -79,7 +79,6 @@ trait Configurable extends ImplicitConversions {
      * @param key Name of value
      * @param default Default value if not found
      * @param submodule Adds to the path
-     * @param required Default false, if true and value is not found this function will raise an exception
      * @param freeVar Default true, if set false value must exist in module
      * @param sample Default null, when set path is prefixed with "samples" -> "sampleID"
      * @param library Default null, when set path is prefixed with "libraries" -> "libraryID"
@@ -88,7 +87,6 @@ trait Configurable extends ImplicitConversions {
     def apply(key: String,
               default: Any = null,
               submodule: String = null,
-              required: Boolean = false,
               freeVar: Boolean = true,
               sample: String = null,
               library: String = null): ConfigValue = {
@@ -100,14 +98,8 @@ trait Configurable extends ImplicitConversions {
         val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
       }
-      if (!contains(key, submodule, freeVar, sample = s, library = l) && d == null) {
-        if (required) {
-          Logging.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 (d == null) return Config.global(m, p, key, freeVar = freeVar)
-      else return Config.global(m, p, key, d, freeVar)
+      if (d == null) Config.global(m, p, key, freeVar = freeVar)
+      else Config.global(m, p, key, d, freeVar)
     }
 
     /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -332,7 +332,9 @@ object ConfigUtils extends Logging {
 
     private def requiredValue(value: ConfigValue): Unit = {
       if (!valueExists(value))
-        throw new IllegalStateException("Value does not exist but is required, key: '" + value.requestIndex.key + "'")
+        throw new IllegalStateException("Value does not exist but is required, key: " + value.requestIndex.key +
+          "  module: " + value.requestIndex.module +
+          (if (value.requestIndex.path != Nil) "  path: " + value.requestIndex.path.mkString("->") else ""))
     }
 
     private def valueExists(value: ConfigValue): Boolean = {