From dbd8c257871162183c250bb01e667c417f74879e Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 28 Oct 2011 16:57:01 -0400 Subject: [PATCH] No more R resources in the DPP updating the DPP to conform with Analyze Covariates changes. --- .../sting/queue/qscripts/DataProcessingPipeline.scala | 6 +----- 1 file changed, 1 insertion(+), 5 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 5e5fd2365..ccbe648d6 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -18,16 +18,13 @@ class DataProcessingPipeline extends QScript { qscript => /**************************************************************************** - * Required Parameters (if default values are not good for you) + * Required Parameters ****************************************************************************/ @Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="i", required=true) var input: File = _ - @Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true) - var R: String = _ - @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true) var reference: File = _ @@ -377,7 +374,6 @@ class DataProcessingPipeline extends QScript { case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates { - this.resources = qscript.R this.recal_file = inRecalFile this.output_dir = outPath.toString this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"