onExecutionDone(jobs, successFlag) added to QScript.

-- This function is called when the Qscript ends, so scripts can overload this function if they want to run some code after all of the jobs have completed

public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -95,7 +95,8 @@ class QCommandLine extends CommandLineProgram with Logging {
   def execute = {
     qGraph.settings = settings
 
-    for (script <- pluginManager.createAllTypes()) {
+    val allQScripts = pluginManager.createAllTypes();
+    for (script <- allQScripts) {
       logger.info("Scripting " + pluginManager.getName(script.getClass.asSubclass(classOf[QScript])))
       loadArgumentsIntoObject(script)
       try {
@@ -108,14 +109,19 @@ class QCommandLine extends CommandLineProgram with Logging {
       logger.info("Added " + script.functions.size + " functions")
     }
 
+    // Execute the job graph
     qGraph.run()
 
+    // walk over each script, calling onExecutionDone
+    for (script <- allQScripts) {
+      script.onExecutionDone(script.functions, qGraph.success)
+    }
+
     if (!qGraph.success) {
       logger.info("Done with errors")
       qGraph.logFailed()
       1
     } else {
-      logger.info("Done")
       0
     }
   }

public/scala/src/org/broadinstitute/sting/queue/QScript.scala

@@ -57,6 +57,14 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    */
   def script()
 
+  /**
+   * A default handler for the onExecutionDone() function.  By default this doesn't do anything
+   * except print out a fine status message.
+   */
+  def onExecutionDone(jobs: List[QFunction], success: Boolean) {
+    logger.info("Script %s with %d total jobs".format(if (success) "completed successfully" else "failed", jobs.size))
+  }
+
   /**
    * The command line functions that will be executed for this QScript.
    */