From 334d66f2b12b50045459f728d2d0343c102f3303 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 26 Jun 2012 14:54:37 -0400 Subject: [PATCH] Updating validation parameter in the DPP users were very confused with the failing validation of their 'unpicarded' bam files. Changed the default to OFF and added an option to turn it on. --- .../sting/queue/qscripts/DataProcessingPipeline.scala | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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))