From 860b172ef122451bb24b1ddbb9e4892022795af2 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Feb 2011 21:13:14 +0000
Subject: [PATCH] Defaulting the MFCP to run without a tear script. Added a
 missing virtual output for the inner FCP, so that Queue can tell a run of the
 FCP is dot-done. Enabled the MCFPTest for the first time, running without the
 tear script.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/MultiFullCallingPipeline.scala   | 17 ++++++++++++-----
 .../MultiFullCallingPipelineTest.scala          |  2 +-
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/scala/qscript/playground/MultiFullCallingPipeline.scala b/scala/qscript/playground/MultiFullCallingPipeline.scala
index d83e0324f..2650f5b5c 100644
--- a/scala/qscript/playground/MultiFullCallingPipeline.scala
+++ b/scala/qscript/playground/MultiFullCallingPipeline.scala
@@ -28,13 +28,16 @@ class MultiFullCallingPipeline extends QScript {
   @Argument(doc="pipeline priority", shortName="PP", required = false)
   var pipelinePriority: Option[Int] = None
 
+  @Argument(doc="run with -tearScript", shortName="TS")
+  var runWithTearScript = false
+
   def script {
     // Global arguments for all pipeline runs
     stingHome = IOUtils.absolute(stingHome)
     val queueJar = new File(stingHome, "dist/Queue.jar")
     val pipelineScript = new File(stingHome, "scala/qscript/playground/FullCallingPipeline.q")
     val gatkJar = new File(stingHome, "dist/GenomeAnalysisTK.jar")
-    val tearScript = new File(stingHome, "R/DataProcessingReport/GetTearsheetStats.R")
+    val tearScript = if (runWithTearScript) new File(stingHome, "R/DataProcessingReport/GetTearsheetStats.R") else null
 
     // Parse the yaml list
     var yamls = List.empty[File]
@@ -64,23 +67,27 @@ class MultiFullCallingPipeline extends QScript {
      * run has produced the passed in output file.
      */
     class RunPipeline(yamlFile: File, lastOutput: File) extends JarCommandLineFunction {
+      private var yamlName = yamlFile.getName.stripSuffix(".yaml")
+
       @Input(doc="output file to wait for", required=false)
       var waitJobOutputFile = lastOutput
 
+      @Output(doc="virtual output file tagging this pipeline as complete")
+      var pipelineComplete = new File(yamlFile.getParentFile, yamlName + ".mfcp")
+
       commandDirectory = yamlFile.getParentFile
       jobOutputFile = IOUtils.absolute(commandDirectory, "queue.out")
       jarFile = queueJar
       memoryLimit = Some(1)
 
-      private var yamlName = yamlFile.getName.stripSuffix(".yaml")
-
       override def commandLine = super.commandLine +
         optional(" -statusTo ", qscript.pipelineStatusTo) +
         optional(" -jobQueue ", qscript.pipelineJobQueue) +
         optional(" -shortJobQueue ", qscript.pipelineShortQueue) +
         optional(" -jobPriority ", qscript.pipelinePriority) +
-        " -S %s --gatkjar %s -tearScript %s -jobProject %s -jobPrefix %s -Y %s -bsub -run"
-          .format(pipelineScript, gatkJar, tearScript, yamlName, yamlName, yamlFile)
+        optional(" -tearScript ", tearScript) +
+        " -S %s --gatkjar %s -jobProject %s -jobPrefix %s -Y %s -bsub -run"
+          .format(pipelineScript, gatkJar, yamlName, yamlName, yamlFile)
 
       override def dotString = "Queue: " + yamlName
     }
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
index ab064b588..987f393f8 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
@@ -54,7 +54,7 @@ class MultiFullCallingPipelineTest {
   final def convertDatasets: Array[Array[AnyRef]] =
     datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray
 
-  @Test(dataProvider="datasets", enabled=false)
+  @Test(dataProvider="datasets")
   def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) = {
     val projectName = dataset.name
     val testName = "MultiFullCallingPipeline-" + projectName