From 0f4be2c4a4ae36d209a50e00f5ba2374aacc0084 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 25 Aug 2011 13:32:03 -0400
Subject: [PATCH] Argument to disable queueJobReport entirely

-- Minor improvements to RodPerformanceGoals
---
 .../src/org/broadinstitute/sting/queue/QCommandLine.scala   | 6 ++++--
 .../broadinstitute/sting/queue/engine/QGraphSettings.scala  | 6 +++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
index 668bd9604..d877575df 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
@@ -115,8 +115,10 @@ class QCommandLine extends CommandLineProgram with Logging {
     // walk over each script, calling onExecutionDone
     for (script <- allQScripts) {
       script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
-      logger.info("Writing JobLogging GATKReport to file " + settings.jobReportFile)
-      QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), settings.jobReportFile)
+      if ( ! settings.disableJobReport ) {
+        logger.info("Writing JobLogging GATKReport to file " + settings.jobReportFile)
+        QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), settings.jobReportFile)
+        // todo -- execute Rscript here once generic RScript execution system is implemented      }
     }
 
     if (!qGraph.success) {
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
index c7a67363d..dbc3e3886 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
@@ -26,8 +26,8 @@ package org.broadinstitute.sting.queue.engine
 
 import java.io.File
 import org.broadinstitute.sting.queue.QSettings
-import org.broadinstitute.sting.commandline.{ArgumentCollection, Argument}
 import org.broadinstitute.sting.queue.util.SystemUtils
+import org.broadinstitute.sting.commandline.{Advanced, ArgumentCollection, Argument}
 
 /**
  * Command line options for a QGraph.
@@ -72,6 +72,10 @@ class QGraphSettings {
   @Argument(fullName="jobReport", shortName="jobReport", doc="File where we will write the Queue job report", required=false)
   var jobReportFile: File = new File("queue_jobreport.gatkreport.txt")
 
+  @Advanced
+  @Argument(fullName="disableJobReport", shortName="disabpleJobReport", doc="If provided, we will not create a job report", required=false)
+  var disableJobReport: Boolean = false
+
   @ArgumentCollection
   val qSettings = new QSettings
 }