cutadapt config parse fix

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -22,9 +22,12 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
   override val versionRegex = """(.*)""".r
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
-  var opt_adapter: Set[String] = Set() + config("adapter")
-  var opt_anywhere: Set[String] = Set() + config("anywhere")
-  var opt_front: Set[String] = Set() + config("front")
+  var opt_adapter: Set[Any] = Set() 
+  if (configContains("adapter")) opt_adapter ++= config("adapter").getList
+  var opt_anywhere: Set[Any] = Set() 
+  if (configContains("anywhere")) opt_anywhere ++= config("anywhere").getList
+  var opt_front: Set[Any] = Set() 
+  if (configContains("front")) opt_front ++= config("front").getList
 
   var opt_discard: Boolean = config("discard")
   var opt_minimum_length: String = config("minimum_length", 1)
@@ -42,4 +45,4 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
     required(fastq_input) +
     required("--output", fastq_output) +
     " > " + required(stats_output)
-}
\ No newline at end of file
+}