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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Matt Hanna 2011-07-19 09:32:01 -04:00
parent 0cec2c6759 9ad5c7dfa4
commit 5d3112c665
13 changed files with 46 additions and 45 deletions
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2
public/packages/PicardPrivate.xml
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@ -7,6 +7,8 @@
<class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
<class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
<class name="edu.mit.broad.picard.util.PasteParser" />
<class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
<class name="edu.mit.broad.picard.util.PicardFileSystemUtil" />
<class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
<class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
<class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />

60
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -72,6 +72,9 @@ 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
/****************************************************************************
* Global Variables
@ -135,7 +138,7 @@ class DataProcessingPipeline extends QScript {
}
}
println("\n\n*** DEBUG ***\n")
println("\n\n*** INPUT FILES ***\n")
// Creating one file for each sample in the dataset
val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
for ((sample, flist) <- sampleTable) {
@ -149,7 +152,7 @@ class DataProcessingPipeline extends QScript {
sampleBamFiles(sample) = sampleFileName
add(joinBams(flist, sampleFileName))
}
println("*** DEBUG ***\n\n")
println("*** INPUT FILES ***\n\n")
return sampleBamFiles.toMap
}
@ -246,7 +249,12 @@ class DataProcessingPipeline extends QScript {
val preValidateLog = swapExt(bam, ".bam", ".pre.validation")
val postValidateLog = swapExt(bam, ".bam", ".post.validation")
add(validate(bam, preValidateLog))
// Validation is an optional step for the BAM file generated after
// alignment and the final bam file of the pipeline.
if (!noValidation) {
add(validate(bam, preValidateLog),
validate(recalBam, postValidateLog))
}
if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
add(target(bam, targetIntervals))
@ -257,8 +265,8 @@ class DataProcessingPipeline extends QScript {
recal(dedupedBam, preRecalFile, recalBam),
cov(recalBam, postRecalFile),
analyzeCovariates(preRecalFile, preOutPath),
analyzeCovariates(postRecalFile, postOutPath),
validate(recalBam, postValidateLog))
analyzeCovariates(postRecalFile, postOutPath))
cohortList :+= recalBam
}
@ -282,6 +290,13 @@ class DataProcessingPipeline extends QScript {
this.isIntermediate = true
}
// General arguments to non-GATK tools
trait ExternalCommonArgs extends CommandLineFunction {
this.memoryLimit = 4
this.isIntermediate = true
}
case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
this.input_file :+= inBams
@ -300,8 +315,8 @@ class DataProcessingPipeline extends QScript {
this.targetIntervals = tIntervals
this.out = outBam
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
if (!indels.isEmpty)
this.rodBind :+= RodBind("indels", "VCF", indels)
if (!qscript.indels.isEmpty)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.consensusDeterminationModel = consensusDeterminationModel
this.compress = 0
this.scatterCount = nContigs
@ -332,7 +347,6 @@ class DataProcessingPipeline extends QScript {
this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration"
}
@ -350,48 +364,41 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
}
case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates {
case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs {
this.input = List(inBam)
this.output = outBam
this.metrics = metricsFile
this.memoryLimit = 6
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".dedup"
this.jobName = queueLogDir + outBam + ".dedup"
}
case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles {
case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles with ExternalCommonArgs {
this.input = inBams
this.output = outBam
this.memoryLimit = 4
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".joinBams"
this.jobName = queueLogDir + outBam + ".joinBams"
}
case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam {
case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs {
this.input = List(inSam)
this.output = outBam
this.sortOrder = sortOrderP
this.memoryLimit = 4
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".sortSam"
this.jobName = queueLogDir + outBam + ".sortSam"
}
case class validate (inBam: File, outLog: File) extends ValidateSamFile {
case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs {
this.input = List(inBam)
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"
}
case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups {
case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs {
this.input = List(inBam)
this.output = outBam
this.RGID = readGroup.id
@ -407,12 +414,7 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".rg"
}
trait BWACommonArgs extends CommandLineFunction {
this.memoryLimit = 4
this.isIntermediate = true
}
case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with BWACommonArgs {
case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with ExternalCommonArgs {
@Input(doc="bam file to be aligned") var bam = inBam
@Output(doc="output sai file") var sai = outSai
def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b " + bam + " > " + sai
@ -420,7 +422,7 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outSai + ".bwa_aln_se"
}
case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with BWACommonArgs {
case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with ExternalCommonArgs {
@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 -t " + bwaThreads + " -q 5 " + reference + " -b" + index + " " + bam + " > " + sai
@ -428,7 +430,7 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
}
case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with BWACommonArgs {
case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs {
@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
@ -437,7 +439,7 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".bwa_sam_se"
}
case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with BWACommonArgs {
case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with ExternalCommonArgs {
@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

12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -20,14 +20,14 @@ class RecalibrateBaseQualities extends QScript {
@Input(doc="input BAM file - or list of BAM files", 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=false)
var R: String = new File("/humgen/gsa-scr1/carneiro/stable/R")
@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", shortName="R", required=false)
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
@Input(doc="Reference fasta file", shortName="R", required=true)
var reference: File = _ // new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=true)
var dbSNP: File = _ // new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
val queueLogDir: String = ".qlog/"
var nContigs: Int = 0

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settings/repository/edu.mit.broad/picard-private-parts-1954.jar
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settings/repository/edu.mit.broad/picard-private-parts-1954.xml~
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1941" status="integration" publication="20110614114100" />
</ivy-module>

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settings/repository/edu.mit.broad/picard-private-parts-1959.jar 100644
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settings/repository/edu.mit.broad/picard-private-parts-1954.xml → settings/repository/edu.mit.broad/picard-private-parts-1959.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1954" status="integration" publication="20110712113100" />
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1959" status="integration" publication="20110718185300" />
</ivy-module>

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settings/repository/net.sf/picard-1.48.889.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.48.889" status="release" />
</ivy-module>

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settings/repository/net.sf/picard-1.48.889.jar → settings/repository/net.sf/picard-1.49.895.jar
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settings/repository/net.sf/picard-1.49.895.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.49.895" status="release" />
</ivy-module>

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settings/repository/net.sf/sam-1.48.889.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.48.889" status="release" />
</ivy-module>

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settings/repository/net.sf/sam-1.48.889.jar → settings/repository/net.sf/sam-1.49.895.jar
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settings/repository/net.sf/sam-1.49.895.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.49.895" status="release" />
</ivy-module>