removing the old processing pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6073 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro
parent
91fb664135
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fbe157137f
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.function.ListWriterFunction
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import scala.io.Source
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class dataProcessing extends QScript {
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qscript =>
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@Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=true)
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var GATKjar: File = _
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@Input(doc="path to AnalyzeCovariates.jar", shortName="ac", required=true)
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var ACJar: File = _
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@Input(doc="path to Picard's MarkDuplicates.jar", shortName="dedup", required=true)
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var dedupJar: File = _
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@Input(doc="path to R resources folder inside the Sting repository", shortName="r", required=true)
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var R: String = _
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@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
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var input: 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="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="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false)
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var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
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@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", shortName="p", required=false)
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var projectName: String = "combined"
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@Input(doc="output path", shortName="outputDir", required=false)
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var outputDir: String = ""
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@Input(doc="the -L interval string to be used by GATK - output bams at interval only", shortName="L", required=false)
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var intervalString: String = ""
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@Input(doc="output bams at intervals only", shortName="intervals", required=false)
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var intervals: File = _
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val queueLogDir: String = ".qlog/"
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// Simple boolean definitions for code clarity
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val knownsOnly: Boolean = true
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val intermediate: Boolean = true
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// General arguments to all programs
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.jarFile = qscript.GATKjar
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this.reference_sequence = qscript.reference
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this.memoryLimit = 4
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this.isIntermediate = true
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}
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def script = {
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var perLaneBamList: List[String] = Nil
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var recalibratedBamList: List[File] = Nil
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// Helpful variables
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val outName: String = qscript.projectName
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val outDir: String = qscript.outputDir
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// BAM files generated by the pipeline
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val bamList: String = outDir + outName + ".list"
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val joinedBams: String = outDir + outName + ".join.bam"
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val cleanedBam: String = outDir + outName + ".clean.bam"
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val fixedBam: String = outDir + outName + ".processed.bam"
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// Accessory files
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val knownTargetIntervals: String = outDir + outName + ".known_indels.intervals"
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val allTargetIntervals: String = outDir + outName + ".all_indels.intervals"
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add(new knownTargets(knownTargetIntervals))
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// Populates the list of per lane bam files to process (single bam or list of bams).
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if (input.endsWith("bam"))
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perLaneBamList :+= input
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else
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for (bam <- Source.fromFile(input).getLines())
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perLaneBamList :+= bam
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perLaneBamList.foreach { perLaneBam =>
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// Helpful variables
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val baseName: String = swapExt(new File(perLaneBam.substring(perLaneBam.lastIndexOf("/")+1)), ".bam", "").toString()
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val baseDir: String = perLaneBam.substring(0, perLaneBam.lastIndexOf("/")+1)
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// BAM files generated by the pipeline
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val cleanedBam: String = baseName + ".clean.bam"
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val dedupedBam: String = baseName + ".clean.dedup.bam"
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val recalBam: String = baseName + ".clean.dedup.recal.bam"
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// Accessory files
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val metricsFile: String = baseName + ".metrics"
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val preRecalFile: String = baseName + ".pre_recal.csv"
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val postRecalFile: String = baseName + ".post_recal.csv"
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val preOutPath: String = baseName + ".pre"
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val postOutPath: String = baseName + ".post"
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add(new clean(perLaneBam, knownTargetIntervals, cleanedBam, knownsOnly, intermediate),
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new dedup(cleanedBam, dedupedBam, metricsFile),
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new cov(dedupedBam, preRecalFile),
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new recal(dedupedBam, preRecalFile, recalBam),
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new cov(recalBam, postRecalFile),
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new analyzeCovariates(preRecalFile, preOutPath),
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new analyzeCovariates(postRecalFile, postOutPath))
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recalibratedBamList :+= new File(recalBam)
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}
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add(new writeList(recalibratedBamList, bamList),
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new joinBams(bamList, joinedBams),
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new allTargets(joinedBams, allTargetIntervals),
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new clean(joinedBams, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate))
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}
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class TargetBase (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
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this.out = new File(outIntervals)
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this.mismatchFraction = 0.0
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.rodBind :+= RodBind("indels", "VCF", indels)
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}
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class knownTargets (outIntervals: String) extends TargetBase(outIntervals) {
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this.jobName = queueLogDir + outIntervals + ".ktarget"
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}
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class allTargets (inBams: String, outIntervals: String) extends TargetBase(outIntervals) {
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this.input_file :+= new File(inBams)
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this.memoryLimit = 6
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this.jobName = queueLogDir + outIntervals + ".atarget"
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}
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class clean (inBams: String, tIntervals: String, outBam: String, knownsOnly: Boolean, intermediate: Boolean) extends IndelRealigner with CommandLineGATKArgs {
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this.input_file :+= new File(inBams)
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this.targetIntervals = new File(tIntervals)
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this.out = new File(outBam)
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
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this.useOnlyKnownIndels = knownsOnly
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this.doNotUseSW = true
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this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
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this.compress = 0
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this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.isIntermediate = intermediate
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this.jobName = queueLogDir + outBam + ".clean"
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if (!intermediate && !qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
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if (!intermediate && qscript.intervals != null) this.intervals :+= qscript.intervals
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}
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class dedup (inBam: String, outBam: String, metricsFile: String) extends PicardBamFunction {
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@Input(doc="fixed bam") var clean: File = new File(inBam)
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@Output(doc="deduped bam") var deduped: File = new File(outBam)
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@Output(doc="deduped bam index") var dedupedIndex: File = new File(outBam + ".bai")
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@Output(doc="metrics file") var metrics: File = new File(metricsFile)
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override def inputBams = List(clean)
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override def outputBam = deduped
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override def commandLine = super.commandLine + " M=" + metricsFile + " CREATE_INDEX=true"
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sortOrder = null
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this.memoryLimit = 6
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this.jarFile = qscript.dedupJar
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this.isIntermediate = true
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this.jobName = queueLogDir + outBam + ".dedup"
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}
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class cov (inBam: String, outRecalFile: String) extends CountCovariates with CommandLineGATKArgs {
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
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this.input_file :+= new File(inBam)
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this.recal_file = new File(outRecalFile)
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this.jobName = queueLogDir + outRecalFile + ".covariates"
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}
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class recal (inBam: String, inRecalFile: String, outBam: String) extends TableRecalibration with CommandLineGATKArgs {
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@Output(doc="recalibrated bam index") var recalIndex: File = new File(outBam + ".bai")
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this.input_file :+= new File (inBam)
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this.recal_file = new File(inRecalFile)
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this.out = new File(outBam)
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this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.index_output_bam_on_the_fly = true
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this.jobName = queueLogDir + outBam + ".recalibration"
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}
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class analyzeCovariates (inRecalFile: String, outPath: String) extends AnalyzeCovariates {
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this.jarFile = qscript.ACJar
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this.resources = qscript.R
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this.recal_file = new File(inRecalFile)
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this.output_dir = outPath
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this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
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}
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class writeList(inBams: List[File], outBamList: String) extends ListWriterFunction {
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this.inputFiles = inBams
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this.listFile = new File(outBamList)
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this.jobName = queueLogDir + outBamList + ".bamList"
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}
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class joinBams(inBams: String, outBam: String) extends PrintReads {
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this.input_file :+= new File(inBams)
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this.out = new File(outBam)
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this.jobName = queueLogDir + inBams + ".joinBams"
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}
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}
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