diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index d71c6ae5d..a961beca1 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -19,10 +19,7 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
 class MethodsDevelopmentCallingPipeline extends QScript {
   qscript =>
 
-  @Argument(shortName="gatk", doc="gatk jar file", required=true)
-  var gatkJarFile: File = _
-
-  @Argument(shortName="outputDir", doc="output directory", required=true)
+  @Argument(shortName="outputDir", doc="output directory", required=false)
   var outputDir: String = "./"
 
   @Argument(shortName="skipCalling", doc="skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)
@@ -185,7 +182,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
 
   trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
     logging_level = "INFO";
-    jarFile = gatkJarFile;
     memoryLimit = 4;
     phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3
   }