diff --git a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala index 8619aa833..8f54ff1db 100755 --- a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala @@ -1,5 +1,6 @@ import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.QScript +import org.broadinstitute.sting.gatk.phonehome.GATKRunReport class MethodsDevelopmentCallingPipeline extends QScript { qscript => @@ -31,7 +32,15 @@ class MethodsDevelopmentCallingPipeline extends QScript { @Argument(shortName="noCut", doc="adds the ApplyVariantCut walker to the pipeline", required=false) var noCut: Boolean = false - trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); } + @Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false) + var LOCAL_ET: Boolean = false + + trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { + logging_level = "INFO"; + jarFile = gatkJarFile; + memoryLimit = Some(3); + phone_home = Some(if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3) + } class Target( val baseName: String,