diff --git a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index cd3d603a1..1d148ac95 100644
--- a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -124,7 +124,7 @@ public class IntervalUtils {
             }
 
         //if we have an empty list, throw an exception.  If they specified intersection and there are no items, this is bad.
-        if (retList == null || retList.size() == 0)
+        if (retList.size() == 0)
                 throw new UserException.BadInput("The INTERSECTION of your -BTI and -L options produced no intervals.");
 
         // we don't need to add the rest of remaining locations, since we know they don't overlap. return what we have
@@ -227,6 +227,31 @@ public class IntervalUtils {
         return contigs;
     }
 
+    /**
+     * Counts the number of interval files an interval list can be split into using scatterIntervalArguments.
+     * @param reference The reference for the intervals.
+     * @param intervals The interval as strings or file paths.
+     * @param splitByContig If true then one contig will not be written to multiple files.
+     * @return The maximum number of parts the intervals can be split into.
+     */
+    public static int countIntervalArguments(File reference, List<String> intervals, boolean splitByContig) {
+        ReferenceDataSource referenceSource = new ReferenceDataSource(reference);
+        List<GenomeLoc> locs = parseIntervalArguments(referenceSource, intervals);
+        int maxFiles = 0;
+        if (splitByContig) {
+            String contig = null;
+            for (GenomeLoc loc: locs) {
+                if (contig == null || !contig.equals(loc.getContig())) {
+                    maxFiles++;
+                    contig = loc.getContig();
+                }
+            }
+        } else {
+            maxFiles = locs.size();
+        }
+        return maxFiles;
+    }
+
     /**
      * Splits an interval list into multiple files.
      * @param reference The reference for the intervals.
diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
index d366085d9..7711759a5 100644
--- a/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
@@ -15,6 +15,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -117,6 +118,16 @@ public class IntervalUtilsUnitTest extends BaseTest {
         Assert.assertEquals(IntervalUtils.distinctContigs(reference, Arrays.asList("chr2:1-1", "chr1:1-1", "chr3:2-2")), Arrays.asList("chr1","chr2","chr3"));
     }
 
+    @Test
+    public void testCountIntervals() {
+        Assert.assertEquals(IntervalUtils.countIntervalArguments(reference, Collections.<String>emptyList(), false), 45);
+        Assert.assertEquals(IntervalUtils.countIntervalArguments(reference, Collections.<String>emptyList(), true), 45);
+        Assert.assertEquals(IntervalUtils.countIntervalArguments(reference, Arrays.asList("chr1", "chr2", "chr3"), false), 3);
+        Assert.assertEquals(IntervalUtils.countIntervalArguments(reference, Arrays.asList("chr1", "chr2", "chr3"), true), 3);
+        Assert.assertEquals(IntervalUtils.countIntervalArguments(reference, Arrays.asList("chr1:1-2", "chr1:4-5", "chr2:1-1", "chr3:2-2"), false), 4);
+        Assert.assertEquals(IntervalUtils.countIntervalArguments(reference, Arrays.asList("chr1:1-2", "chr1:4-5", "chr2:1-1", "chr3:2-2"), true), 3);
+    }
+
     @Test
     public void testBasicScatter() {
         GenomeLoc chr1 = genomeLocParser.parseGenomeInterval("chr1");
diff --git a/scala/qscript/examples/ExampleCountLoci.scala b/scala/qscript/examples/ExampleCountLoci.scala
new file mode 100644
index 000000000..d3e1add25
--- /dev/null
+++ b/scala/qscript/examples/ExampleCountLoci.scala
@@ -0,0 +1,33 @@
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+
+/**
+ * An introductory pipeline with integration tests testing the MD5 of the @Output.
+ */
+class ExampleCountLoci extends QScript {
+  @Input(doc="The path to the GenomeAnalysisTK.jar file.", shortName="gatk")
+  var gatkJar: File = null
+
+  @Input(doc="The reference file for the bam files.", shortName="R")
+  var referenceFile: File = null
+
+  @Input(doc="One or more bam files.", shortName="I")
+  var bamFiles: List[File] = Nil
+
+  @Input(doc="Intervals to traverse.", shortName="L", required=false)
+  var intervals: List[String] = Nil
+
+  @Output
+  var out: File = _
+
+  def script = {
+    val countLoci = new CountLoci
+    countLoci.jarFile = gatkJar
+    countLoci.reference_sequence = referenceFile
+    countLoci.input_file = bamFiles
+    countLoci.intervalsString = intervals
+    countLoci.out = out
+    countLoci.memoryLimit = Some(1)
+    add(countLoci)
+  }
+}
diff --git a/scala/qscript/playground/fullCallingPipeline.q b/scala/qscript/playground/fullCallingPipeline.q
index 6799a47a9..805b79632 100755
--- a/scala/qscript/playground/fullCallingPipeline.q
+++ b/scala/qscript/playground/fullCallingPipeline.q
@@ -1,19 +1,14 @@
 
-import java.io.PrintWriter
 import org.broadinstitute.sting.commandline.ArgumentSource
 import org.broadinstitute.sting.datasources.pipeline.Pipeline
-import org.broadinstitute.sting.gatk.DownsampleType
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
 import org.broadinstitute.sting.queue.extensions.samtools._
+import org.broadinstitute.sting.queue.function.ListWriterFunction
 import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction}
-import org.broadinstitute.sting.queue.util.IOUtils
 import org.broadinstitute.sting.queue.QScript
 import collection.JavaConversions._
-import org.broadinstitute.sting.utils.exceptions.UserException
-import org.broadinstitute.sting.utils.interval.IntervalUtils
 import org.broadinstitute.sting.utils.yaml.YamlUtils
-import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
 
 class fullCallingPipeline extends QScript {
   qscript =>
@@ -105,9 +100,6 @@ class fullCallingPipeline extends QScript {
       //val seq = qscript.machine
       //val expKind = qscript.protocol
 
-      // get max num contigs for indel cleaning parallelism, plus 1 for -L unmapped
-      val numContigs = IntervalUtils.distinctContigs(qscript.pipeline.getProject.getReferenceFile).size + 1
-
       for ( sample <- recalibratedSamples ) {
         val sampleId = sample.getId
         // put unclean bams in unclean genotypers in advance, create the extension files
@@ -136,7 +128,7 @@ class fullCallingPipeline extends QScript {
         realigner.targetIntervals = targetCreator.out
         realigner.intervals = Nil
         realigner.intervalsString = Nil
-        realigner.scatterCount = num_cleaner_scatter_jobs min numContigs
+        realigner.scatterCount = num_cleaner_scatter_jobs
         realigner.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
         realigner.rodBind :+= RodBind("indels", "VCF", swapExt(realigner.reference_sequence.getParentFile, realigner.reference_sequence, "fasta", "1kg_pilot_indels.vcf"))
 
@@ -384,21 +376,9 @@ class fullCallingPipeline extends QScript {
     // 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
+    val writeBamList = new ListWriterFunction
+    writeBamList.inputFiles = bamFiles
+    writeBamList.listFile = listOfBams
     writeBamList.analysisName = base + "_BamList"
     writeBamList.jobOutputFile = new File(".queue/logs/SNPCalling/bamlist.out")
 
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
index 25d3bb699..5e3384020 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
-import org.broadinstitute.sting.commandline.ArgumentSource
 import org.broadinstitute.sting.utils.interval.IntervalUtils
 import java.io.File
 import collection.JavaConversions._
 import org.broadinstitute.sting.queue.util.IOUtils
 import org.broadinstitute.sting.queue.function.scattergather.{CloneFunction, ScatterGatherableFunction, ScatterFunction}
 import org.broadinstitute.sting.queue.function.{QFunction, InProcessFunction}
+import org.broadinstitute.sting.commandline.{Output, ArgumentSource}
 
 /**
  * An interval scatter function.
@@ -15,7 +15,7 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
   var splitByContig = false
 
   /** The total number of clone jobs that will be created. */
-  private var scatterCount: Int = _
+  var scatterCount: Int = _
 
   /** The reference sequence for the GATK function. */
   private var referenceSequence: File = _
@@ -32,6 +32,9 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
   /** Whether the laster scatter job should also include any unmapped reads. */
   private var includeUnmapped: Boolean = _
 
+  @Output(doc="Scattered intervals")
+  var scatterParts: List[File] = Nil
+
   /**
    * Checks if the function is scatter gatherable.
    * @param originalFunction Function to check.
@@ -54,7 +57,6 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
     val gatk = originalFunction.asInstanceOf[CommandLineGATK]
     this.intervalsField = QFunction.findField(originalFunction.getClass, "intervals")
     this.intervalsStringField = QFunction.findField(originalFunction.getClass, "intervalsString")
-    this.scatterCount = originalFunction.scatterCount
     this.referenceSequence = gatk.reference_sequence
     if (gatk.intervals.isEmpty && gatk.intervalsString.isEmpty) {
       this.intervals ++= IntervalUtils.distinctContigs(this.referenceSequence).toList
@@ -64,11 +66,14 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
       this.intervals ++= gatk.intervalsString.filterNot(interval => IntervalUtils.isUnmapped(interval))
       this.includeUnmapped = gatk.intervalsString.exists(interval => IntervalUtils.isUnmapped(interval))
     }
+
+    val maxScatterCount = IntervalUtils.countIntervalArguments(this.referenceSequence, this.intervals, this.splitByContig)
+    this.scatterCount = maxScatterCount min originalFunction.scatterCount
   }
 
   def initCloneInputs(cloneFunction: CloneFunction, index: Int) = {
     cloneFunction.setFieldValue(this.intervalsField, List(new File("scatter.intervals")))
-    if (index == scatterCount && includeUnmapped)
+    if (index == this.scatterCount && this.includeUnmapped)
       cloneFunction.setFieldValue(this.intervalsStringField, List("unmapped"))
     else
       cloneFunction.setFieldValue(this.intervalsStringField, List.empty[String])
diff --git a/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
new file mode 100644
index 000000000..f60302ef4
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
@@ -0,0 +1,33 @@
+package org.broadinstitute.sting.queue.function
+
+import org.broadinstitute.sting.commandline.{Input, Output}
+import java.io.{PrintWriter, File}
+import org.apache.commons.io.IOUtils
+
+/**
+ * Writes a list of inputs to an output file.
+ * Custom formats can override addFile.
+ */
+class ListWriterFunction extends InProcessFunction {
+  @Input(doc="input files") var inputFiles: List[File] = Nil
+  @Output(doc="output file") var listFile: File = _
+
+  def run {
+    val writer = new PrintWriter(listFile)
+    try {
+      for (inputFile <- inputFiles)
+        addFile(writer, inputFile)
+    } finally {
+      IOUtils.closeQuietly(writer)
+    }
+  }
+
+  /**
+   * Adds the inputFile to the output list.
+   * @param writer Output file.
+   * @param inputFile File to add to the output file.
+   */
+  def addFile(writer: PrintWriter, inputFile: File) {
+    writer.println(inputFile.toString)
+  }
+}
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
index 86e9ab921..790c575bf 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.queue.function.scattergather
 
 import java.io.File
-import org.broadinstitute.sting.commandline.{Input, Output}
+import org.broadinstitute.sting.commandline.Input
 import org.broadinstitute.sting.queue.function.QFunction
 
 /**
@@ -11,9 +11,6 @@ trait ScatterFunction extends QFunction {
   @Input(doc="Original inputs to scatter")
   var originalInputs: Set[File] = _
 
-  @Output(doc="Scattered parts of the original inputs, one set per temp directory")
-  var scatterParts: List[File] = Nil
-
   /**
    * Returns true if the scatter function can scatter this original function.
    * @param originalFunction The original function to check.
@@ -27,6 +24,11 @@ trait ScatterFunction extends QFunction {
    */
   def setScatterGatherable(originalFunction: ScatterGatherableFunction)
 
+  /**
+   * After a call to setScatterGatherable(), returns the number of clones that should be created.
+   */
+  def scatterCount: Int
+
   /**
    * Initializes the input fields for the clone function.
    * The input values should be set to their defaults
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
index 4609f6f18..a4b31b519 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
@@ -11,7 +11,7 @@ import org.broadinstitute.sting.queue.QException
  */
 trait ScatterGatherableFunction extends CommandLineFunction {
 
-  /** Number of parts to scatter the function into" */
+  /** Maximum number of parts to scatter the function into. */
   var scatterCount: Int = 1
 
   /** scatter gather directory */
@@ -79,10 +79,13 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     initScatterFunction(scatterFunction)
     functions :+= scatterFunction
 
+    // Ask the scatter function how many clones to create.
+    val numClones = scatterFunction.scatterCount
+
     // Create the gather functions for each output field
     var gatherFunctions = Map.empty[ArgumentSource, GatherFunction]
     var gatherOutputs = Map.empty[ArgumentSource, File]
-    var gatherAddOrder = this.scatterCount + 2
+    var gatherAddOrder = numClones + 2
     for (gatherField <- outputFieldsWithValues) {
       val gatherFunction = this.newGatherFunction(gatherField)
       val gatherOutput = getFieldFile(gatherField)
@@ -100,7 +103,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
 
     // Create the clone functions for running the parallel jobs
     var cloneFunctions = List.empty[CloneFunction]
-    for (i <- 1 to this.scatterCount) {
+    for (i <- 1 to numClones) {
       val cloneFunction = this.newCloneFunction()
 
       syncFunction(cloneFunction)
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
index a7dfae4f3..b4c210ccf 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
@@ -11,6 +11,43 @@ import java.text.SimpleDateFormat
 import org.broadinstitute.sting.{WalkerTest, BaseTest}
 
 object PipelineTest {
+
+  /** The path to the current Sting directory.  Useful when specifying Sting resources. */
+  val currentStingDir = new File(".").getAbsolutePath
+
+  /** The path to the current build of the GATK jar in the currentStingDir. */
+  val currentGATK = new File(currentStingDir, "dist/GenomeAnalysisTK.jar")
+
+  /**
+   * Returns the top level output path to this test.
+   * @param testName The name of the test passed to PipelineTest.executeTest()
+   * @return the top level output path to this test.
+   */
+  def testDir(testName: String) = "pipelinetests/%s/".format(testName)
+
+  /**
+   * Returns the directory where relative output files will be written for this test.
+   * @param testName The name of the test passed to PipelineTest.executeTest()
+   * @return the directory where relative output files will be written for this test.
+   */
+  def runDir(testName: String) = testDir(testName) + "run/"
+
+  /**
+   * Returns the directory where temp files will be written for this test.
+   * @param testName The name of the test passed to PipelineTest.executeTest()
+   * @return the directory where temp files will be written for this test.
+   */
+  def tempDir(testName: String) = testDir(testName) + "temp/"
+
+  /**
+   * Encapsulates a file MD5
+   * @param testName The name of the test also passed to PipelineTest.executeTest().
+   * @param filePath The file path of the output file, relative to the directory the pipeline is run in.
+   * @param md5 The expected MD5
+   * @return a file md5 that can be appended to the PipelineTestSpec.fileMD5s
+   */
+  def fileMD5(testName: String, filePath: String, md5: String) = (new File(runDir(testName) + filePath), md5)
+
   private var runningCommandLines = Set.empty[QCommandLine]
 
   private val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/"
@@ -34,10 +71,11 @@ object PipelineTest {
     var failed = 0
     for ((file, expectedMD5) <- fileMD5s) {
       val calculatedMD5 = BaseTest.testFileMD5(name, file, expectedMD5, false)
-      failed += 1
+      if (expectedMD5 != "" && expectedMD5 != calculatedMD5)
+        failed += 1
     }
     if (failed > 0)
-      Assert.fail("%d MD5%s did not match.".format(failed, TextFormatUtils.plural(failed)))
+      Assert.fail("%d of %d MD5%s did not match.".format(failed, fileMD5s.size, TextFormatUtils.plural(failed)))
   }
 
   private def validateEval(name: String, evalSpec: PipelineTestEvalSpec) {
@@ -124,11 +162,6 @@ object PipelineTest {
     }
   }
 
-  val currentDir = new File(".").getAbsolutePath
-  def testDir(testName: String) = "pipelinetests/%s/".format(testName)
-  def runDir(testName: String) = testDir(testName) + "run/"
-  def tempDir(testName: String) = testDir(testName) + "temp/"
-
   Runtime.getRuntime.addShutdownHook(new Thread {
     /** Cleanup as the JVM shuts down. */
     override def run {
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
new file mode 100644
index 000000000..59d4d5162
--- /dev/null
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
@@ -0,0 +1,20 @@
+package org.broadinstitute.sting.queue.pipeline.examples
+
+import org.testng.annotations.Test
+import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.BaseTest
+
+class ExampleCountLociPipelineTest {
+  @Test
+  def testCountLoci {
+    var testName = "countloci"
+    var testOut = "count.out"
+    val spec = new PipelineTestSpec
+    // TODO: Use a variable instead of "hour"
+    spec.args = "-S scala/qscript/examples/ExampleCountLoci.scala -gatk %s -R %s -I %s -o %s -jobQueue hour".format(
+      PipelineTest.currentGATK, BaseTest.hg18Reference, BaseTest.validationDataLocation + "small_bam_for_countloci.bam", testOut
+    )
+    spec.fileMD5s += PipelineTest.fileMD5(testName, testOut, "67823e4722495eb10a5e4c42c267b3a6")
+    PipelineTest.executeTest(testName, spec)
+  }
+}
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
index 6b43479bb..70b188c3a 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
@@ -9,8 +9,6 @@ class HelloWorldPipelineTest {
     var testName = "helloworld"
     val spec = new PipelineTestSpec
     spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld -jobQueue hour"
-    // TODO: working example of MD5 usage.
-    // spec.fileMD5s += new File(PipelineTest.runDir(testName) + "hello.out") -> "0123456789abcdef0123456789abcdef"
     PipelineTest.executeTest(testName, spec)
   }
 }
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
index 51d1f999e..7e8335c42 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
@@ -93,8 +93,8 @@ class FullCallingPipelineTest {
     var pipelineCommand = ("-retry 1 -S scala/qscript/playground/fullCallingPipeline.q" +
             " -jobProject %s -Y %s" +
             " -tearScript %s/R/DataProcessingReport/GetTearsheetStats.R" +
-            " --gatkjar %s/dist/GenomeAnalysisTK.jar")
-            .format(projectName, yamlFile, PipelineTest.currentDir, PipelineTest.currentDir)
+            " --gatkjar %s")
+            .format(projectName, yamlFile, PipelineTest.currentStingDir, PipelineTest.currentGATK)
 
     if (!dataset.runIndelRealigner) {
       pipelineCommand += " -skipCleaning"