Rename modules to reflect the fact that they're really packages in their own right.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2638 348d0f76-0448-11de-a6fe-93d51630548a

packages/GATK-GSA-Pipeline.xml

@@ -7,13 +7,13 @@
     <name>GATK-GSA-Pipeline</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibrationModule.xml</module>
+    <module>QualityScoresRecalibration.xml</module>
-    <module>LocalRealignmentAroundIndelsModule.xml</module>
+    <module>LocalRealignmentAroundIndels.xml</module>
-    <module>UnifiedGenotyperModule.xml</module>
+    <module>UnifiedGenotyper.xml</module>
-    <module>VariantFiltrationModule.xml</module>
+    <module>VariantFiltration.xml</module>
-    <module>VariantAnnotatorModule.xml</module>
+    <module>VariantAnnotator.xml</module>
-    <module>VariantEvalModule.xml</module>
+    <module>VariantEval.xml</module>
-    <module>FindContaminatingReadGroupsModule.xml</module>
+    <module>FindContaminatingReadGroups.xml</module>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>

packages/GATK-Picard.xml

@@ -8,11 +8,11 @@
     <name>GATK-Picard</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibrationModule.xml</module>
+    <module>QualityScoresRecalibration.xml</module>
-    <module>LocalRealignmentAroundIndelsModule.xml</module>
+    <module>LocalRealignmentAroundIndels.xml</module>
-    <module>UnifiedGenotyperModule.xml</module>
+    <module>UnifiedGenotyper.xml</module>
-    <module>VariantFiltrationModule.xml</module>
+    <module>VariantFiltration.xml</module>
-    <module>VariantAnnotatorModule.xml</module>
+    <module>VariantAnnotator.xml</module>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>

packages/GenomeAnalysisTK.xml

@@ -5,12 +5,12 @@
     <name>GenomeAnalysisTK</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibrationModule.xml</module>
+    <module>QualityScoresRecalibration.xml</module>
-    <module>LocalRealignmentAroundIndelsModule.xml</module>
+    <module>LocalRealignmentAroundIndels.xml</module>
-    <module>UnifiedGenotyperModule.xml</module>
+    <module>UnifiedGenotyper.xml</module>
-    <module>VariantFiltrationModule.xml</module>
+    <module>VariantFiltration.xml</module>
-    <module>VariantAnnotatorModule.xml</module>
+    <module>VariantAnnotator.xml</module>
-    <module>VCFValidatorModule.xml</module>
+    <module>VCFValidator.xml</module>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>