Resolving simple conflicts in the data processing pipeline.
Conflicts: public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
This commit is contained in:
Mauricio Carneiro
commit
9ad5c7dfa4
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@ -72,6 +72,9 @@ class DataProcessingPipeline extends QScript {
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@Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
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var bwaThreads: Int = 1
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@Input(doc="Dont perform validation on the BAM files", fullName="no_validation", shortName="nv", required=false)
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var noValidation: Boolean = false
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/****************************************************************************
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* Global Variables
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@ -135,7 +138,7 @@ class DataProcessingPipeline extends QScript {
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}
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}
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println("\n\n*** DEBUG ***\n")
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println("\n\n*** INPUT FILES ***\n")
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// Creating one file for each sample in the dataset
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val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
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for ((sample, flist) <- sampleTable) {
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@ -149,7 +152,7 @@ class DataProcessingPipeline extends QScript {
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sampleBamFiles(sample) = sampleFileName
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add(joinBams(flist, sampleFileName))
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}
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println("*** DEBUG ***\n\n")
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println("*** INPUT FILES ***\n\n")
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return sampleBamFiles.toMap
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}
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@ -246,7 +249,12 @@ class DataProcessingPipeline extends QScript {
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val preValidateLog = swapExt(bam, ".bam", ".pre.validation")
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val postValidateLog = swapExt(bam, ".bam", ".post.validation")
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add(validate(bam, preValidateLog))
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// Validation is an optional step for the BAM file generated after
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// alignment and the final bam file of the pipeline.
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if (!noValidation) {
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add(validate(bam, preValidateLog),
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validate(recalBam, postValidateLog))
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}
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if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
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add(target(bam, targetIntervals))
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@ -257,8 +265,8 @@ class DataProcessingPipeline extends QScript {
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recal(dedupedBam, preRecalFile, recalBam),
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cov(recalBam, postRecalFile),
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analyzeCovariates(preRecalFile, preOutPath),
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analyzeCovariates(postRecalFile, postOutPath),
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validate(recalBam, postValidateLog))
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analyzeCovariates(postRecalFile, postOutPath))
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cohortList :+= recalBam
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}
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@ -282,6 +290,13 @@ class DataProcessingPipeline extends QScript {
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this.isIntermediate = true
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}
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// General arguments to non-GATK tools
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trait ExternalCommonArgs extends CommandLineFunction {
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this.memoryLimit = 4
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this.isIntermediate = true
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}
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case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
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if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
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this.input_file :+= inBams
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@ -300,8 +315,8 @@ class DataProcessingPipeline extends QScript {
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this.targetIntervals = tIntervals
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this.out = outBam
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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if (!indels.isEmpty)
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this.rodBind :+= RodBind("indels", "VCF", indels)
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if (!qscript.indels.isEmpty)
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this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
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this.consensusDeterminationModel = consensusDeterminationModel
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this.compress = 0
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this.scatterCount = nContigs
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@ -332,7 +347,6 @@ class DataProcessingPipeline extends QScript {
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this.isIntermediate = false
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this.analysisName = queueLogDir + outBam + ".recalibration"
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this.jobName = queueLogDir + outBam + ".recalibration"
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}
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@ -350,48 +364,41 @@ class DataProcessingPipeline extends QScript {
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this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
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}
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case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates {
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case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs {
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this.input = List(inBam)
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this.output = outBam
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this.metrics = metricsFile
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this.memoryLimit = 6
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".dedup"
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this.jobName = queueLogDir + outBam + ".dedup"
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}
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case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles {
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case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles with ExternalCommonArgs {
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this.input = inBams
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this.output = outBam
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this.memoryLimit = 4
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".joinBams"
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this.jobName = queueLogDir + outBam + ".joinBams"
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}
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case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam {
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case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs {
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this.input = List(inSam)
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this.output = outBam
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this.sortOrder = sortOrderP
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this.memoryLimit = 4
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".sortSam"
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this.jobName = queueLogDir + outBam + ".sortSam"
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}
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case class validate (inBam: File, outLog: File) extends ValidateSamFile {
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case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs {
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this.input = List(inBam)
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this.output = outLog
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this.maxRecordsInRam = 100000
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this.REFERENCE_SEQUENCE = qscript.reference
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this.memoryLimit = 4
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this.isIntermediate = false
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this.analysisName = queueLogDir + outLog + ".validate"
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this.jobName = queueLogDir + outLog + ".validate"
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}
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case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups {
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case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs {
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this.input = List(inBam)
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this.output = outBam
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this.RGID = readGroup.id
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@ -407,12 +414,7 @@ class DataProcessingPipeline extends QScript {
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this.jobName = queueLogDir + outBam + ".rg"
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}
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trait BWACommonArgs extends CommandLineFunction {
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this.memoryLimit = 4
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this.isIntermediate = true
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}
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case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with BWACommonArgs {
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case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with ExternalCommonArgs {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Output(doc="output sai file") var sai = outSai
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def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b " + bam + " > " + sai
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@ -420,7 +422,7 @@ class DataProcessingPipeline extends QScript {
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this.jobName = queueLogDir + outSai + ".bwa_aln_se"
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}
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case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with BWACommonArgs {
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case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with ExternalCommonArgs {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Output(doc="output sai file for 1st mating pair") var sai = outSai1
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def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b" + index + " " + bam + " > " + sai
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@ -428,7 +430,7 @@ class DataProcessingPipeline extends QScript {
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this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
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}
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case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with BWACommonArgs {
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case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Input(doc="bwa alignment index file") var sai = inSai
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@Output(doc="output aligned bam file") var alignedBam = outBam
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@ -437,7 +439,7 @@ class DataProcessingPipeline extends QScript {
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this.jobName = queueLogDir + outBam + ".bwa_sam_se"
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}
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case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with BWACommonArgs {
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case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with ExternalCommonArgs {
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@Input(doc="bam file to be aligned") var bam = inBam
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@Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1
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@Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2
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@ -20,14 +20,14 @@ class RecalibrateBaseQualities extends QScript {
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@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
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var input: File = _
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@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=false)
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var R: String = new File("/humgen/gsa-scr1/carneiro/stable/R")
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@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true)
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var R: String = _
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@Input(doc="Reference fasta file", shortName="R", required=false)
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var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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@Input(doc="Reference fasta file", shortName="R", required=true)
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var reference: File = _ // new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
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var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
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@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=true)
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var dbSNP: File = _ // new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
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val queueLogDir: String = ".qlog/"
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var nContigs: Int = 0
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