Merge branch 'patch-varscan' into 'develop'

Patch varscan

This pull request fixes an error caused by incorrect passing of the Java flags to the VarScan command used in Gentrap. For local runs, it has no effect. However, these are important for cluster runs.

See merge request !137

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
   }
 }