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quick memory upgrade to BWA classes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6074 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-06-23 20:53:32 +00:00
parent fbe157137f
commit 087a25d9e3
1 changed files with 13 additions and 24 deletions
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37
scala/qscript/core/DataProcessingPipeline.scala
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@ -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"
}