diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index c269a7af7..f5321e824 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -56,6 +56,15 @@ class fullCallingPipeline extends QScript {
   @Input(doc="Number of jobs to scatter indel genotyper",shortName="indelScatter",required=false)
   var num_indel_scatter_jobs = 5
 
+  @Input(doc="ADPR script")
+  var adprScript: File = _
+
+  @Input(doc="Sequencing maching name (for use by adpr)")
+  var machine: String = _
+
+  @Input(doc="Sequencing experiement type (for use by adpr)--Whole_Exome, Whole_Genome, or Hybrid_Selection")
+  var protocol: String = _
+
   private var pipeline: Pipeline = _
 
   trait CommandLineGATKArgs extends CommandLineGATK {
@@ -65,6 +74,8 @@ class fullCallingPipeline extends QScript {
   }
 
 
+
+
   // ------------ SETUP THE PIPELINE ----------- //
 
 
@@ -76,7 +87,9 @@ class fullCallingPipeline extends QScript {
     // there are commands that use all the bam files
     val recalibratedSamples = qscript.pipeline.getSamples
             .filter(_.getBamFiles.contains("recalibrated"))
-
+    val adprRScript = qscript.adprScript
+    val seq = qscript.machine
+    val expKind = qscript.protocol
     for ( sample <- recalibratedSamples ) {
 
       // put unclean bams in unclean genotypers
@@ -166,12 +179,12 @@ class fullCallingPipeline extends QScript {
             .toList
 
     // actually make calls
-    endToEnd(uncleanedBase,recalibratedBamFiles)
+    endToEnd(uncleanedBase,recalibratedBamFiles, adprRscript, seq, expKind)
     // COMMENT THIS NEXT LINE TO AVOID CALLING ON CLEANED FILES
-    endToEnd(cleanedBase,cleanBamFiles)
+    endToEnd(cleanedBase,cleanBamFiles, adprRscript, seq, expKind)
   }
 
-  def endToEnd(base: String, bamFiles: List[File]) = {
+  def endToEnd(base: String, bamFiles: List[File], adprthing: File, seqinfo: String, exptype: String) = {
 
     // step through the un-indel-cleaned graph:
     // 1a. call snps and indels
@@ -306,16 +319,43 @@ class fullCallingPipeline extends QScript {
     eval.rodBind :+= RodBind("evalOptimized", "VCF", cut.out)
     eval.rodBind :+= RodBind("evalHandFiltered", "VCF", handFilter.out)
     eval.evalModule ++= List("CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator")
-    eval.out = new File(base+".eval")
+    eval.reportLocation = new File(base+".eval")
+    eval.reportType = "R"
     eval.analysisName = base+"_VariantEval"
 
     add(snps)
 
+    // 5. Run the ADPR and make pretty stuff
+
+    val adpr = new CommandLineFunction{
+     @Input(doc="Dependent files") var dependents: File = _
+     @Output(doc="Automated Data processing report") var out: File = _
+      var setname: String
+      var protocol: String
+      var sequencer: String
+      var scriptloc: File
+      def commandLine = "Rscript %s %s %s %s"
+        .format(scriptloc, setname, protocol, sequencer)
+    }
+
+    adpr.setname = base
+    adpr.scriptloc = adprthing
+    adpr.sequencer = seqinfo
+    adpr.protocol = exptype
+    adpr.dependents = eval.reportLocation
+    adpr.out = new File(base + "_adpr.pdf")
+    adpr.analysisName = base + "_ADPR"
+    //In order for ADPR to finish successfully, a squid file for both the lane and sample level data needs to be
+    // produced, reformatted and named <projectBase>_lanes.txt or <projectBase>_samps.txt, respectively. These files
+    // to be in the working directory. When database access is ready, this and the protocol and sequencer parameters of
+    //the r script will go away.
+
+
     for ( igv2 <- indelGenotypers ) {
       add(igv2)
     }
 
-    add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval)
+    add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval,adpr)
 
   }