From 4d611e53e73f8902c51ef58bb4caee9a6012d095 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 20 Jan 2011 06:08:45 +0000
Subject: [PATCH] Passing the ADPR R script to FCPTest. Changed the FCP.q to
 use an InProcessFunction work around the -runDir issue GSA-420. Tested the
 FCPTest using the following dotkits and "ant clean pipelinetest
 -Dpipeline.run=run":   - R-2.11   - Oracle-full-client   -
 .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5029 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../qscript/playground/fullCallingPipeline.q  | 37 +++++++++++++------
 .../pipeline/FullCallingPipelineTest.scala    |  4 +-
 2 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/scala/qscript/playground/fullCallingPipeline.q b/scala/qscript/playground/fullCallingPipeline.q
index 62a3d7bdf..df76a8f46 100755
--- a/scala/qscript/playground/fullCallingPipeline.q
+++ b/scala/qscript/playground/fullCallingPipeline.q
@@ -48,7 +48,7 @@ class fullCallingPipeline extends QScript {
   var skip_cleaning = false
 
   @Input(doc="ADPR script", shortName ="tearScript", required=true)
-  var adprthing: File = _
+  var tearScript: File = _
 
   //@Input(doc="Sequencing maching name (for use by adpr)")
   //var machine: String = _
@@ -200,18 +200,10 @@ class fullCallingPipeline extends QScript {
     }
   }
 
-  //def endToEnd(base: String, bamType: String, adprthing: File, seqinfo: String, exptype: String) = {
   def endToEnd(base: String, bamType: String) = {
 
     val samples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains(bamType)).toList
     val bamFiles = samples.map(_.getBamFiles.get(bamType))
-    val listOfBams =  new File(base +".BamFiles.list")
-
-    val writer = new PrintWriter(listOfBams)
-      for (bamFile <- bamFiles){
-        writer.println(bamFile.toString)
-      }
-      writer.close()
 
     // step through the un-indel-cleaned graph:
     // 1a. call snps and indels
@@ -385,7 +377,28 @@ class fullCallingPipeline extends QScript {
     }
     add(snps)
 
-    // 5. Run the ADPR and make pretty stuff
+    // 5. Make the bam list
+    val listOfBams =  new File(base +".BamFiles.list")
+
+    class BamListWriter extends InProcessFunction {
+      @Input(doc="bamFiles") var bamFiles: List[File] = Nil
+      @Output(doc="bamList") var bamList: File = _
+
+      def run {
+        val writer = new PrintWriter(bamList)
+        for (bamFile <- bamFiles)
+          writer.println(bamFile.toString)
+        writer.close()
+      }
+    }
+
+    val writeBamList = new BamListWriter
+    writeBamList.bamFiles = bamFiles
+    writeBamList.bamList = listOfBams
+    writeBamList.analysisName = base + "_BamList"
+    writeBamList.jobOutputFile = new File(".queue/logs/SNPCalling/bamlist.out")
+
+    // 6. Run the ADPR and make pretty stuff
 
     class rCommand extends CommandLineFunction{
       @Argument(doc="R script")
@@ -404,7 +417,7 @@ class fullCallingPipeline extends QScript {
 
     val adpr = new rCommand
      adpr.bamlist = listOfBams
-     adpr.script = adprthing
+     adpr.script = tearScript
      adpr.evalroot = eval.reportLocation
      adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out")
      adpr.tearsheet = new File("SnpCalls", base + ".tearsheet.pdf")
@@ -416,6 +429,6 @@ class fullCallingPipeline extends QScript {
       add(igv2)
     }
 
-    add(mergeIndels,annotated,masker,handFilter,eval,adpr)
+    add(mergeIndels,annotated,masker,handFilter,eval,writeBamList,adpr)
   }
 }
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
index 6eb1f4cd6..6d3e4d63d 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
@@ -90,10 +90,12 @@ class FullCallingPipelineTest extends BaseTest {
     var cleanType = "cleaned"
 
     // Run the pipeline with the expected inputs.
+    val currentDir = new File(".").getAbsolutePath
     var pipelineCommand = ("-retry 1 -S scala/qscript/playground/fullCallingPipeline.q" +
             " -jobProject %s -Y %s -refseqTable %s" +
+            " -tearScript %s/R/DataProcessingReport/GetTearsheetStats.R" +
             " --gatkjar %s/dist/GenomeAnalysisTK.jar")
-            .format(projectName, yamlFile, dataset.refseq, new File(".").getAbsolutePath)
+            .format(projectName, yamlFile, dataset.refseq, currentDir, currentDir)
 
     if (!dataset.runIndelRealigner) {
       pipelineCommand += " -skipCleaning"