Java jobs now show diffrent version output in summary

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core.summary
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunctionTrait, BiopetCommandLineFunction, SampleLibraryTag, BiopetQScript }
+import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.extensions.Md5sum
 
 import scala.collection.mutable
@@ -104,8 +104,13 @@ trait SummaryQScript extends BiopetQScript {
     }
 
     //Automatic checksums
-    for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles)
+    for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles) {
       addChecksum(file)
+      summarizable match {
+        case f: BiopetJavaCommandLineFunction => if (f.jarFile != null) addChecksum(f.jarFile)
+        case _                                =>
+      }
+    }
 
     for ((_, file) <- this.summaryFiles)
       addChecksum(file)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.summary
 import java.io.{ FileInputStream, PrintWriter, File }
 import java.security.MessageDigest
 
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunctionTrait, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, SampleLibraryTag }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.function.{ QFunction, InProcessFunction }
@@ -56,7 +56,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
       val executables: Map[String, Any] = {
         (for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield {
           f match {
-            case f: BiopetCommandLineFunctionTrait => {
+            case f: BiopetJavaCommandLineFunction => {
+              f.configName -> Map("version" -> f.getVersion,
+                "java_md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
+                "jar_md5" -> SummaryQScript.md5sumCache.getOrElse(f.jarFile, None))
+            }
+            case f: BiopetCommandLineFunction => {
               f.configName -> Map("version" -> f.getVersion,
                 "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None))
             }