gatk-3.8/packages/GATK-GSA-Pipeline.xml

<?xml version="1.0" encoding="UTF-8"?>
<!-- NOTE: Uses playground.
     ant clean playground package -Dexecutable=GATK-GSA-Pipeline -->
<package>
  <name>GATK-GSA-Pipeline</name>
  <executable>
    <name>GATK-GSA-Pipeline</name>
    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
    <properties>StingText.properties</properties>
    <module>QualityScoresRecalibrationModule.xml</module>
    <module>LocalRealignmentAroundIndelsModule.xml</module>
    <module>UnifiedGenotyperModule.xml</module>
    <module>VariantFiltrationModule.xml</module>
    <module>VariantAnnotatorModule.xml</module>
    <module>VariantEvalModule.xml</module>
    <module>FindContaminatingReadGroupsModule.xml</module>
    <dependencies>
      <!-- Filters -->
      <package>org.broadinstitute.sting.gatk.filters</package>
    </dependencies>
  </executable>
</package>