Fix incorrectly passed java flags for piped VarScan command

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

@@ -63,20 +63,27 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
     override def cmdLine: String = required(executable) + required("-vP") + required("""\t\t""")
   }
 
-  private def varscan = new Mpileup2cns(wrapper.root) {
+  private val varscan = new Mpileup2cns(wrapper.root) {
     strandFilter = Option(0)
     outputVcf = Option(1)
   }
 
-  private def compress = new Bgzip(wrapper.root) {
-    this.output = wrapper.output
-  }
+  private val compress = new Bgzip(wrapper.root)
 
-  private def index = new Tabix(wrapper.root) {
+  private val index = new Tabix(wrapper.root) {
     input = compress.output
     p = Option("vcf")
   }
 
+  override def freezeFieldValues(): Unit = {
+    varscan.output = Option(new File(wrapper.output.toString.stripSuffix(".gz")))
+    compress.input = List(varscan.output.get)
+    compress.output = this.output
+    super.freezeFieldValues()
+    varscan.qSettings = this.qSettings
+    varscan.freezeFieldValues()
+  }
+
   override def beforeGraph: Unit = {
     require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
   }
@@ -85,6 +92,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
     // FIXME: manual trigger of commandLine for version retrieval
     mpileup.commandLine
     mpileup.cmdPipe + " | " + fixMpileup.commandLine + " | " + removeEmptyPile.commandLine + " | " +
-      varscan.commandLine + " | " + compress.commandLine + " && " + index.commandLine
+      varscan.commandLine + " && " + compress.commandLine + " && " + index.commandLine
   }
 }