Removed default use of @Output syntax.

If compile completes for QScripts, sending runtime errors during execute.

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

@@ -110,6 +110,9 @@ class QCommandLine extends CommandLineProgram with Logging {
    * functions, and then builds and runs a QGraph based on the dependencies.
    */
   def execute = {
+    var success = false
+    var result = 1
+    try {
       ClassFieldCache.parsingEngine = this.parser
 
       if (settings.qSettings.runName == null)
@@ -166,7 +169,6 @@ class QCommandLine extends CommandLineProgram with Logging {
       qGraph.run()
 
       val functionsAndStatus = qGraph.getFunctionsAndStatus
-    val success = qGraph.success
 
       // walk over each script, calling onExecutionDone
       for (script <- allQScripts) {
@@ -180,14 +182,7 @@ class QCommandLine extends CommandLineProgram with Logging {
       logger.info("Writing final jobs report...")
       qGraph.writeJobsReport()
 
-    if (!success) {
+      if (qGraph.success) {
-      logger.info("Done with errors")
-      qGraph.logFailed()
-      for (commandPlugin <- allCommandPlugins)
-        if (commandPlugin.statusMessenger != null)
-          commandPlugin.statusMessenger.exit("Done with errors: %s".format(qGraph.formattedStatusCounts))
-      1
-    } else {
         if (settings.run) {
           allQScripts.foreach(_.pushOutputs())
           for (commandPlugin <- allCommandPlugins)
@@ -197,8 +192,21 @@ class QCommandLine extends CommandLineProgram with Logging {
               commandPlugin.statusMessenger.done(allInputs, allOutputs)
             }
         }
-      0
+        success = true
+        result = 0
       }
+    } finally {
+      if (!success) {
+        logger.info("Done with errors")
+        qGraph.logFailed()
+        if (settings.run) {
+          for (commandPlugin <- allCommandPlugins)
+            if (commandPlugin.statusMessenger != null)
+              commandPlugin.statusMessenger.exit("Done with errors: %s".format(qGraph.formattedStatusCounts))
+        }
+      }
+    }
+    result
   }
 
   /**

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

@@ -124,49 +124,26 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
   }
 
   /**
-   * Pull all remote files to the local disk.
+   * Pull all remote files to the local disk
    */
   def pullInputs() {
-    val inputs = ClassFieldCache.getFieldFiles(this, inputFields)
-    for (remoteFile <- filterRemoteFiles(inputs)) {
-      logger.info("Pulling %s from %s".format(remoteFile.getAbsolutePath, remoteFile.remoteDescription))
-      remoteFile.pullToLocal()
-    }
   }
 
   /**
-   * Push all remote files from the local disk.
+   * Push all remote files from the local disk
    */
   def pushOutputs() {
-    val outputs = ClassFieldCache.getFieldFiles(this, outputFields)
-    for (remoteFile <- filterRemoteFiles(outputs)) {
-      logger.info("Pushing %s to %s".format(remoteFile.getAbsolutePath, remoteFile.remoteDescription))
-      remoteFile.pushToRemote()
-    }
   }
 
   /**
-   * List out the remote outputs
+   * @return the inputs or null if there are no inputs
-   * @return the RemoteFile outputs by argument source
    */
-  def remoteInputs: Map[String, Seq[RemoteFile]] = tagMap(remoteFieldMap(inputFields))
+  def remoteInputs: AnyRef = null
 
   /**
-   * List out the remote outputs
+   * @return the outputs or null if there are no outputs
-   * @return the RemoteFile outputs by argument source
    */
-  def remoteOutputs: Map[String, Seq[RemoteFile]] = tagMap(remoteFieldMap(outputFields))
+  def remoteOutputs: AnyRef = null
-
-  private def tagMap(remoteFieldMap: Map[ArgumentSource, Seq[RemoteFile]]): Map[String, Seq[RemoteFile]] = {
-    remoteFieldMap.collect{ case (k, v) => ClassFieldCache.fullName(k) -> v }.toMap
-  }
-
-  private def remoteFieldMap(fields: Seq[ArgumentSource]): Map[ArgumentSource, Seq[RemoteFile]] = {
-    fields.map(field => (field -> filterRemoteFiles(ClassFieldCache.getFieldFiles(this, field)))).filter(tuple => !tuple._2.isEmpty).toMap
-  }
-
-  private def filterRemoteFiles(fields: Seq[File]): Seq[RemoteFile] =
-    fields.filter(field => field != null && field.isInstanceOf[RemoteFile]).map(_.asInstanceOf[RemoteFile])
 
   /** The complete list of fields. */
   def functionFields: Seq[ArgumentSource] = ClassFieldCache.classFunctionFields(this.getClass)

public/scala/src/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala

@@ -7,7 +7,7 @@ import org.broadinstitute.sting.queue.util.RemoteFile
  */
 trait QStatusMessenger {
   def started()
-  def done(inputs: Seq[Map[String, Seq[RemoteFile]]], outputs: Seq[Map[String, Seq[RemoteFile]]])
+  def done(inputs: Seq[_], outputs: Seq[_])
   def exit(message: String)
 
   def started(job: String)