Tests

public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala

 package nl.lumc.sasc.biopet.pipelines.gwastest
 
 import java.io.File
+import java.util
 
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, BiopetQScript }
 import nl.lumc.sasc.biopet.extensions.gatk.{ SelectVariants, CombineVariants }
@@ -9,29 +10,36 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
 import org.broadinstitute.gatk.queue.QScript
 
+import scala.collection.JavaConversions._
+
 /**
  * Created by pjvanthof on 16/03/16.
  */
 class GwasTest(val root: Configurable) extends QScript with BiopetQScript with Reference {
   def this() = this(null)
 
-  lazy val inputVcf: Option[File] = config("input_vcf")
+  val inputVcf: Option[File] = config("input_vcf")
 
-  lazy val phenotypeFile: File = config("phenotype_file")
+  val phenotypeFile: File = config("phenotype_file")
 
   case class GensInput(genotypes: File, info: Option[File], contig: String)
-  lazy val inputGens: Option[List[GensInput]] = if (inputVcf.isDefined) None
+
+  val inputBlaGens: List[GensInput] = if (inputVcf.isDefined) List[GensInput]()
   else {
-    if (config.contains("input_gens")) {
-      val gens: List[Any] = configValue2list(config("input_gens"))
-      Some(gens.map {
+    println("blabla")
+      config("input_gens", default = Nil).asList.map(x => x match {
         case value: Map[String, Any] =>
           GensInput(new File(value("genotypes").toString),
             value.get("info").map(x => new File(x.toString)),
             value("contig").toString)
+        case value: util.LinkedHashMap[_, _] =>
+          GensInput(new File(value("genotypes").toString),
+            value.toMap.get("info").map(x => new File(x.toString)),
+            value("contig").toString)
+        case _ => throw new IllegalArgumentException
       })
-    } else None
-  }
+    List[GensInput]()
+    }
 
   /** Init for pipeline */
   def init(): Unit = {
@@ -40,12 +48,12 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
   /** Pipeline itself */
   def biopetScript(): Unit = {
     val vcfFile: File = inputVcf.getOrElse {
-      val gens = inputGens.getOrElse(throw new IllegalArgumentException("No vcf file or gens files defined in config"))
+      require(inputBlaGens.nonEmpty, "No vcf file or gens files defined in config")
       val outputDirGens = new File(outputDir, "gens_to_vcf")
       val cv = new CombineVariants(this)
       cv.outputFile = new File(outputDirGens, "merge.gens.vcf.gz")
       cv.setKey = "null"
-      gens.foreach { gen =>
+      inputBlaGens.foreach { gen =>
         val gensToVcf = new GensToVcf(this)
         gensToVcf.inputGens = gen.genotypes
         gensToVcf.inputInfo = gen.info