diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index e26541e98..677d973f5 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -68,8 +68,8 @@ class DataProcessingPipeline extends QScript { @Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false) var bwaThreads: Int = 1 - @Input(doc="Dont perform validation on the BAM files", fullName="no_validation", shortName="nv", required=false) - var noValidation: Boolean = false + @Input(doc="Perform validation on the BAM files", fullName="validation", shortName="vs", required=false) + var validation: Boolean = false /**************************************************************************** @@ -268,7 +268,7 @@ class DataProcessingPipeline extends QScript { // Validation is an optional step for the BAM file generated after // alignment and the final bam file of the pipeline. - if (!noValidation) { + if (validation) { for (sampleFile <- bamList) add(validate(sampleFile, preValidateLog), validate(recalBam, postValidateLog))