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Quick updates to the data processing pipeline after successfully cleaning the papuans. It now scatter gathers everything and runs in the hour queue for low pass data. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5546 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-31 21:13:33 +00:00
parent dac1309dbd
commit 20344a27b4
1 changed files with 8 additions and 5 deletions
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13
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
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@ -37,7 +37,7 @@ class dataProcessingV2 extends QScript {
@Input(doc="path to Picard's MergeSamFiles.jar", fullName="path_to_merge_jar", shortName="merge", required=false) @Input(doc="path to Picard's MergeSamFiles.jar", fullName="path_to_merge_jar", shortName="merge", required=false)
var mergeBamJar: File = new File("/seq/software/picard/current/bin/MergeSamFiles.jar") var mergeBamJar: File = new File("/seq/software/picard/current/bin/MergeSamFiles.jar")
@Input(doc="path to Picard's ValidateSam.jar", fullName="path_to_validate_jar", shortName="validate", required=false) @Input(doc="path to Picard's ValidateSamFile.jar", fullName="path_to_validate_jar", shortName="validate", required=false)
var validateSamJar: File = new File("/seq/software/picard/current/bin/ValidateSamFile.jar") var validateSamJar: File = new File("/seq/software/picard/current/bin/ValidateSamFile.jar")
@Input(doc="Reference fasta file", fullName="reference", shortName="R", required=false) @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=false)
@ -50,16 +50,16 @@ class dataProcessingV2 extends QScript {
****************************************************************************/ ****************************************************************************/
@Input(doc="path to Picard's RevertSam.jar", fullName="path_to_revert_jar", shortName="revert", required=false) @Input(doc="path to Picard's RevertSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_revert_jar", shortName="revert", required=false)
var revertSamJar: File = _ var revertSamJar: File = _
@Input(doc="path to Picard's SortSam.jar", fullName="path_to_sort_jar", shortName="sort", required=false) @Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
var sortSamJar: File = _ var sortSamJar: File = _
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false) @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
var bwaPath: File = _ var bwaPath: File = _
@Input(doc="dbsnp ROD to use (VCF)", fullName="dbsnp", shortName="D", required=false) @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=false)
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf") var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false) @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
@ -294,6 +294,7 @@ class dataProcessingV2 extends QScript {
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam this.input_file :+= inBam
this.recal_file = outRecalFile this.recal_file = outRecalFile
this.scatterCount = nContigs
this.jobQueue = "gsa" // should take this out once scatter gather is available. this.jobQueue = "gsa" // should take this out once scatter gather is available.
this.analysisName = queueLogDir + outRecalFile + ".covariates" this.analysisName = queueLogDir + outRecalFile + ".covariates"
this.jobName = queueLogDir + outRecalFile + ".covariates" this.jobName = queueLogDir + outRecalFile + ".covariates"
@ -309,7 +310,8 @@ class dataProcessingV2 extends QScript {
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString) if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals else if (qscript.intervals != null) this.intervals :+= qscript.intervals
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! 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!
this.index_output_bam_on_the_fly = true this.index_output_bam_on_the_fly = true // todo -- implemente @gather for BAM index
// this.scatterCount = nContigs
this.isIntermediate = false this.isIntermediate = false
this.jobQueue = "gsa" // should take this out once scatter gather is available. this.jobQueue = "gsa" // should take this out once scatter gather is available.
this.analysisName = queueLogDir + outBam + ".recalibration" this.analysisName = queueLogDir + outBam + ".recalibration"
@ -333,6 +335,7 @@ class dataProcessingV2 extends QScript {
case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamFunction { case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamFunction {
@Input(doc="fixed bam") var clean = inBam @Input(doc="fixed bam") var clean = inBam
@Output(doc="deduped bam") var deduped = outBam @Output(doc="deduped bam") var deduped = outBam
@Output(doc="deduped bam index") var dedupedIndex = new File(outBam + "bai")
@Output(doc="metrics file") var metrics = metricsFile @Output(doc="metrics file") var metrics = metricsFile
override def inputBams = List(clean) override def inputBams = List(clean)
override def outputBam = deduped override def outputBam = deduped