diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index 724518142..2417e5620 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -106,7 +106,7 @@ class DataProcessingPipeline extends QScript {
   // Because the realignment only happens after these scripts are executed, in case you are using
   // bwa realignment, this function will operate over the original bam files and output over the
   // (to be realigned) bam files.
-  def createSampleFiles(bamFiles: List[File], realignedBamFiles: List[File]): Map[String, File] = {
+  def createSampleFiles(bamFiles: List[File], realignedBamFiles: List[File]): Map[String, List[File]] = {
 
     // Creating a table with SAMPLE information from each input BAM file
     val sampleTable = scala.collection.mutable.Map.empty[String, List[File]]
@@ -131,24 +131,25 @@ class DataProcessingPipeline extends QScript {
           sampleTable(sample) :+= rBam
       }
     }
+    return sampleTable.toMap
 
-    println("\n\n*** INPUT FILES ***\n")
-    // Creating one file for each sample in the dataset
-    val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
-    for ((sample, flist) <- sampleTable) {
-
-      println(sample + ":")
-      for (f <- flist)
-        println (f)
-      println()
-
-      val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".list")
-      sampleBamFiles(sample) = sampleFileName
-      add(writeList(flist, sampleFileName))
-    }
-    println("*** INPUT FILES ***\n\n")
-
-    return sampleBamFiles.toMap
+//    println("\n\n*** INPUT FILES ***\n")
+//    // Creating one file for each sample in the dataset
+//    val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
+//    for ((sample, flist) <- sampleTable) {
+//
+//      println(sample + ":")
+//      for (f <- flist)
+//        println (f)
+//      println()
+//
+//      val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".list")
+//      sampleBamFiles(sample) = sampleFileName
+//      //add(writeList(flist, sampleFileName))
+//    }
+//    println("*** INPUT FILES ***\n\n")
+//
+//    return sampleBamFiles.toMap
   }
 
   // Rebuilds the Read Group string to give BWA
@@ -224,7 +225,10 @@ class DataProcessingPipeline extends QScript {
 
 
   def script = {
+    // final output list of processed bam files
+    var cohortList: List[File] = List()
 
+    // sets the model for the Indel Realigner
     cleanModelEnum = getIndelCleaningModel()
 
     // keep a record of the number of contigs in the first bam file in the list
@@ -233,28 +237,19 @@ class DataProcessingPipeline extends QScript {
 
     val realignedBAMs = if (useBWApe || useBWAse) {performAlignment(bams)} else {revertBams(bams)}
 
-    // Generate a BAM file per sample joining all per lane files if necessary
-    val sampleBAMFiles: Map[String, File] = createSampleFiles(bams, realignedBAMs)
+    // generate a BAM file per sample joining all per lane files if necessary
+    val sampleBAMFiles: Map[String, List[File]] = createSampleFiles(bams, realignedBAMs)
 
-    // Final output list of processed bam files
-    var cohortList: List[File] = List()
-
-    // Simple progress report
-    println("\nFound the following samples: ")
-    for ((sample, file) <- sampleBAMFiles)
-      println("\t" + sample + " -> " + file)
-    println("\n")
-
-    // If this is a 'knowns only' indel realignment run, do it only once for all samples.
+    // if this is a 'knowns only' indel realignment run, do it only once for all samples.
     val globalIntervals = new File(outputDir + projectName + ".intervals")
     if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY)
       add(target(null, globalIntervals))
 
-    // Put each sample through the pipeline
-    for ((sample, sampleFile) <- sampleBAMFiles) {
-      val bam = if (sampleFile.endsWith(".list")) {swapExt(sampleFile, ".list", ".bam")} else {sampleFile}
+    // put each sample through the pipeline
+    for ((sample, bamList) <- sampleBAMFiles) {
 
       // BAM files generated by the pipeline
+      val bam        = new File(qscript.projectName + "." + sample + ".bam")
       val cleanedBam = swapExt(bam, ".bam", ".clean.bam")
       val dedupedBam = swapExt(bam, ".bam", ".clean.dedup.bam")
       val recalBam   = swapExt(bam, ".bam", ".clean.dedup.recal.bam")
@@ -272,15 +267,16 @@ class DataProcessingPipeline extends QScript {
 
       // Validation is an optional step for the BAM file generated after
       // alignment and the final bam file of the pipeline.
-      if (!noValidation && sampleFile.endsWith(".bam")) {        // todo -- implement validation for .list BAM files
+      if (!noValidation) {
+        for (sampleFile <- bamList)
         add(validate(sampleFile, preValidateLog),
             validate(recalBam, postValidateLog))
       }
 
       if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
-        add(target(sampleFile, targetIntervals))
+        add(target(bamList, targetIntervals))
 
-      add(clean(sampleFile, targetIntervals, cleanedBam),
+      add(clean(bamList, targetIntervals, cleanedBam),
           dedup(cleanedBam, dedupedBam, metricsFile),
           cov(dedupedBam, preRecalFile),
           recal(dedupedBam, preRecalFile, recalBam),
@@ -320,9 +316,9 @@ class DataProcessingPipeline extends QScript {
       this.maxRecordsInRam = 100000
   }
 
-  case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
+  case class target (inBams: List[File], outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
     if (cleanModelEnum != ConsensusDeterminationModel.KNOWNS_ONLY)
-      this.input_file :+= inBams
+      this.input_file = inBams
     this.out = outIntervals
     this.mismatchFraction = 0.0
     this.known :+= qscript.dbSNP
@@ -333,8 +329,8 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outIntervals + ".target"
   }
 
-  case class clean (inBams: File, tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
-    this.input_file :+= inBams
+  case class clean (inBams: List[File], tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
+    this.input_file = inBams
     this.targetIntervals = tIntervals
     this.out = outBam
     this.known :+= qscript.dbSNP