Fix reference in varscan

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 /** Ad-hoc extension for VarScan variant calling that involves 6-command pipe */
 // FIXME: generalize piping instead of building something by hand like this!
 // Better to do everything quick and dirty here rather than something half-implemented with the objects
-class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction { wrapper =>
+class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction with Reference { wrapper =>
 
   override def configName = "customvarscan"
 
@@ -36,7 +36,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
   var input: File = null
 
   @Input(doc = "Reference FASTA file", required = true)
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Output(doc = "Output VCF file", required = true)
   var output: File = null
@@ -49,7 +49,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
     this.input = List(wrapper.input)
     override def configName = wrapper.configName
     disableBaq = true
-    reference = config("reference")
     depth = Option(1000000)
     outputMappingQuality = true
   }
@@ -92,7 +91,9 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
   }
 
   override def beforeGraph(): Unit = {
+    super.beforeGraph()
     require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
+    if (reference == null) reference = referenceFasta()
   }
 
   def cmdLine: String = {