From d35c7d10296b23141ace607fa1580b71b3b898e5 Mon Sep 17 00:00:00 2001 From: carneiro Date: Tue, 19 Apr 2011 16:35:24 +0000 Subject: [PATCH] - minor changes to the 'justclean' script to handle the Trio Cleaning. - fixing a bug on single ended BWA option of the data processing pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5662 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/oneoffs/carneiro/dataProcessingV2.scala | 2 +- scala/qscript/oneoffs/carneiro/justClean.scala | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala b/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala index 7665d1824..5b74c1534 100755 --- a/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala +++ b/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala @@ -442,7 +442,7 @@ class dataProcessingV2 extends QScript { @Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1 @Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2 @Output(doc="output aligned bam file") var alignedBam = outBam - def commandLine = bwaPath + " samse " + reference + " " + sai1 + " " + sai2 + " " + bam + " -r " + readGroup + " > " + alignedBam + def commandLine = bwaPath + " sampe " + reference + " " + sai1 + " " + sai2 + " " + bam + " -r " + readGroup + " > " + alignedBam this.isIntermediate = true this.analysisName = queueLogDir + outBam + ".bwa_sam_pe" this.jobName = queueLogDir + outBam + ".bwa_sam_pe" diff --git a/scala/qscript/oneoffs/carneiro/justClean.scala b/scala/qscript/oneoffs/carneiro/justClean.scala index e2e8a7153..1ecc4bd5a 100755 --- a/scala/qscript/oneoffs/carneiro/justClean.scala +++ b/scala/qscript/oneoffs/carneiro/justClean.scala @@ -59,14 +59,14 @@ class justClean extends QScript { clean.reference_sequence = reference clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) clean.rodBind :+= RodBind("indels", "VCF", indels) - clean.doNotUseSW = true + clean.doNotUseSW = false clean.compress = 0 - clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly! +// clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly! clean.jobName = queueLogDir + outBam + ".clean" clean.jarFile = GATKjar - clean.memoryLimit = 12 + clean.memoryLimit = 6 clean.scatterCount = 84 - add(clean); + add(target, clean); } }