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 2f0715ae9..b860358ca 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -25,9 +25,6 @@ class MethodsDevelopmentCallingPipeline extends QScript { @Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false) var noIndels: Boolean = false - @Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false) - var LOCAL_ET: Boolean = false - @Argument(shortName="mbq", doc="The minimum Phred-Scaled quality score threshold to be considered a good base.", required=false) var minimumBaseQuality: Int = -1 @@ -203,7 +200,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; memoryLimit = 4; - phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3 + phone_home = GATKRunReport.PhoneHomeOption.NO_ET } def bai(bam: File) = new File(bam + ".bai")