first step towards the new sample based processing pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5471 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro
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package oneoffs.carneiro
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
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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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class dataProcessingV2 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 Picard's MergeSamFiles.jar", shortName="merge", required=true)
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var mergeBamJar: 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: File = _
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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="Perform cleaning on knowns only", shortName="knowns", required=false)
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var knownsOnly: Boolean = false
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@Input(doc="Perform cleaning on using Smith Waterman", shortName="sw", required=false)
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var useSW: Boolean = false
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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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def script = {
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// Helpful variables
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val outName: String = qscript.outputDir + qscript.projectName
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// BAM files generated by the pipeline
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val joinedBams = new File(outName + ".join.bam")
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val cleanedBam = new File(outName + ".clean.bam")
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val dedupedBam = new File(outName + ".clean.dedup.bam")
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val recalBam = new File(outName + ".clean.dedup.recal.bam")
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// Accessory files
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val targetIntervals = new File(outName + ".intervals")
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val metricsFile = new File(outName + ".metrics")
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val preRecalFile = new File(outName + ".pre_recal.csv")
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val postRecalFile = new File(outName + ".post_recal.csv")
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val preOutPath = new File(outName + ".pre")
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val postOutPath = new File(outName + ".post")
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//todo -- process bam headers to compile bamLists of samples.
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add(joinBams(input, joinedBams),
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target(joinedBams, targetIntervals),
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clean(joinedBams, targetIntervals, cleanedBam),
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dedup(cleanedBam, dedupedBam, metricsFile),
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cov(dedupedBam, preRecalFile),
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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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}
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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 = Some(4)
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this.isIntermediate = true
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}
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case class joinBams (inBams: File, outBam: File) extends PicardBamJarFunction {
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@Input(doc="input bam list") var join = inBams
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@Output(doc="joined bam") var joined = outBam
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@Output(doc="joined bam index") var joinedIndex = new File(outBam + "bai")
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override def inputBams = List(join)
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override def outputBam = joined
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override def commandLine = super.commandLine + " CREATE_INDEX=true"
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this.memoryLimit = Some(6)
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this.jarFile = qscript.mergeBamJar
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this.isIntermediate = true
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this.jobName = queueLogDir + outBam + ".joinBams"
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}
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case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
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if (!knownsOnly)
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this.input_file :+= inBams
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this.out = outIntervals
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this.mismatchFraction = Some(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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this.jobName = queueLogDir + outIntervals + ".target"
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}
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case class clean (inBams: File, tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
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this.input_file :+= inBams
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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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this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
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this.useOnlyKnownIndels = knownsOnly
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this.doNotUseSW = useSW
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this.compress = Some(0)
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this.U = Some(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.jobName = queueLogDir + outBam + ".clean"
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}
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case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamJarFunction {
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@Input(doc="fixed bam") var clean = inBam
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@Output(doc="deduped bam") var deduped = outBam
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@Output(doc="deduped bam index") var dedupedIndex = new File(outBam + ".bai")
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@Output(doc="metrics file") var metrics = 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 = Some(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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case class cov (inBam: File, outRecalFile: File) 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 :+= inBam
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this.recal_file = outRecalFile
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this.jobName = queueLogDir + outRecalFile + ".covariates"
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}
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case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
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@Output(doc="recalibrated bam index") var recalIndex = new File(outBam + ".bai")
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this.input_file :+= inBam
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this.recal_file = inRecalFile
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this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
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this.out = outBam
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if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
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else if (qscript.intervals != null) this.intervals :+= qscript.intervals
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this.U = Some(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 = Some(true)
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this.jobName = queueLogDir + outBam + ".recalibration"
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}
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case class analyzeCovariates (inRecalFile: File, outPath: File) 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 = inRecalFile
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this.output_dir = outPath.toString
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this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
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}
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case class writeList(inBams: List[File], outBamList: File) extends ListWriterFunction {
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this.inputFiles = inBams
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this.listFile = outBamList
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this.jobName = queueLogDir + outBamList + ".bamList"
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}
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}
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