From 087a25d9e3622321f3fb9a093615a56a02b50fc1 Mon Sep 17 00:00:00 2001 From: carneiro Date: Thu, 23 Jun 2011 20:53:32 +0000 Subject: [PATCH] quick memory upgrade to BWA classes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6074 348d0f76-0448-11de-a6fe-93d51630548a --- .../qscript/core/DataProcessingPipeline.scala | 37 +++++++------------ 1 file changed, 13 insertions(+), 24 deletions(-) diff --git a/scala/qscript/core/DataProcessingPipeline.scala b/scala/qscript/core/DataProcessingPipeline.scala index 74b18118c..cad19bd23 100755 --- a/scala/qscript/core/DataProcessingPipeline.scala +++ b/scala/qscript/core/DataProcessingPipeline.scala @@ -29,22 +29,6 @@ class DataProcessingPipeline extends QScript { @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true) var reference: File = _ -// @Input(doc="path to GenomeAnalysisTK.jar", fullName="path_to_gatk_jar", shortName="gatk", required=false) -// var GATKjar: File = _ -// -// @Input(doc="path to AnalyzeCovariates.jar", fullName="path_to_ac_jar", shortName="ac", required=false) -// var ACJar: File = _ -// -// @Input(doc="path to Picard's MarkDuplicates.jar", fullName="path_to_dedup_jar", shortName="dedup", required=false) -// var dedupJar: File = _ -// -// @Input(doc="path to Picard's MergeSamFiles.jar", fullName="path_to_merge_jar", shortName="merge", required=false) -// var mergeBamJar: File = _ -// -// @Input(doc="path to Picard's ValidateSamFile.jar", fullName="path_to_validate_jar", shortName="validate", required=false) -// var validateSamJar: File = _ - - /**************************************************************************** @@ -395,6 +379,7 @@ class DataProcessingPipeline extends QScript { case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles { this.input = inBams this.output = outBam + this.memoryLimit = 4 this.isIntermediate = true this.analysisName = queueLogDir + outBam + ".joinBams" this.jobName = queueLogDir + outBam + ".joinBams" @@ -403,6 +388,7 @@ class DataProcessingPipeline extends QScript { case class sortSam (inSam: File, outBam: File) extends SortSam { this.input = List(inSam) this.output = outBam + this.memoryLimit = 4 this.isIntermediate = true this.analysisName = queueLogDir + outBam + ".sortSam" this.jobName = queueLogDir + outBam + ".sortSam" @@ -413,6 +399,7 @@ class DataProcessingPipeline extends QScript { this.output = outLog this.maxRecordsInRam = 100000 this.REFERENCE_SEQUENCE = qscript.reference + this.memoryLimit = 4 this.isIntermediate = false this.analysisName = queueLogDir + outLog + ".validate" this.jobName = queueLogDir + outLog + ".validate" @@ -429,46 +416,48 @@ class DataProcessingPipeline extends QScript { this.RGPL = readGroup.pl this.RGPU = readGroup.pu this.RGSM = readGroup.sm + this.memoryLimit = 4 this.isIntermediate = true this.analysisName = queueLogDir + outBam + ".rg" this.jobName = queueLogDir + outBam + ".rg" } - case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction { + trait BWACommonArgs extends CommandLineFunction { + this.memoryLimit = 4 + this.isIntermediate = true + } + + case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with BWACommonArgs { @Input(doc="bam file to be aligned") var bam = inBam @Output(doc="output sai file") var sai = outSai def commandLine = bwaPath + " aln -q 5 " + reference + " -b " + bam + " > " + sai - this.isIntermediate = true this.analysisName = queueLogDir + outSai + ".bwa_aln_se" this.jobName = queueLogDir + outSai + ".bwa_aln_se" } - case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction { + case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with BWACommonArgs { @Input(doc="bam file to be aligned") var bam = inBam @Output(doc="output sai file for 1st mating pair") var sai = outSai1 def commandLine = bwaPath + " aln -q 5 " + reference + " -b" + index + " " + bam + " > " + sai - this.isIntermediate = true this.analysisName = queueLogDir + outSai1 + ".bwa_aln_pe1" this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1" } - case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction { + case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with BWACommonArgs { @Input(doc="bam file to be aligned") var bam = inBam @Input(doc="bwa alignment index file") var sai = inSai @Output(doc="output aligned bam file") var alignedBam = outBam def commandLine = bwaPath + " samse " + reference + " " + sai + " " + bam + " > " + alignedBam - this.isIntermediate = true this.analysisName = queueLogDir + outBam + ".bwa_sam_se" this.jobName = queueLogDir + outBam + ".bwa_sam_se" } - case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction { + case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with BWACommonArgs { @Input(doc="bam file to be aligned") var bam = inBam @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 + " sampe " + reference + " " + sai1 + " " + sai2 + " " + bam + " " + bam + " > " + alignedBam - this.isIntermediate = true this.analysisName = queueLogDir + outBam + ".bwa_sam_pe" this.jobName = queueLogDir + outBam + ".bwa_sam_pe" }