Simplifications: removed command-line arguments to control SNP cluster filter parameters. Infer the number of contigs to scatter indel cleaning from the contig list (which we should get rid of too). Changed the PY argument to just Y for specifying the path to the YAML file. Cleaned up command-line argument documentation. See http://iwww.broadinstitute.org/gsa/wiki/index.php/Queue-based_pipeline for a list of remaining issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4356 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
9820a12fa5
commit
bcc09f5d8c
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@ -1,3 +1,4 @@
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import net.sf.picard.reference.FastaSequenceFile
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import org.broadinstitute.sting.datasources.pipeline.Pipeline
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import org.broadinstitute.sting.gatk.DownsampleType
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import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
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@ -12,59 +13,47 @@ import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
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class fullCallingPipeline extends QScript {
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qscript =>
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@Argument(doc="contigIntervals", shortName="contigIntervals")
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@Argument(doc="list of contigs in the reference over which indel-cleaning jobs should be scattered (ugly)", shortName="contigIntervals")
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var contigIntervals: File = _
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@Argument(doc="numContigs", shortName="numContigs")
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var numContigs: Int = _
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@Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
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var yamlFile: File = _
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@Argument(fullName="pipeline_yaml", shortName="PY", doc="Pipeline YAML file")
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var pipelineYamlFile: File = _
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@Input(doc="trigger", shortName="trigger", required=false)
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@Input(doc="path to trigger track (for UnifiedGenotyper)", shortName="trigger", required=false)
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var trigger: File = _
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@Input(doc="compCEU",shortName="ceu",required=false)
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var comp1KGCEU: File = _
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@Input(doc="refseqTable", shortName="refseqTable")
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@Input(doc="path to refseqTable (for GenomicAnnotator)", shortName="refseqTable")
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var refseqTable: File = _
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@Input(doc="Picard FixMateInformation.jar. At the Broad this can be found at /seq/software/picard/current/bin/FixMateInformation.jar. Outside the Broad see http://picard.sourceforge.net/")
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var picardFixMatesJar: File = _
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@Input(doc="path to Picard FixMateInformation.jar. See http://picard.sourceforge.net/ .", required=false)
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var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
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@Input(doc="gatk jar")
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@Input(doc="path to GATK jar")
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var gatkJar: File = _
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@Input(doc="SNP cluster filter -- number SNPs",shortName="snpsInCluster",required=false)
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var snpsInCluster = 3
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@Input(doc="SNP cluster filter -- window size",shortName="snpClusterWindow",required=false)
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var snpClusterWindow = 10
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@Input(doc="target titv for recalibration",shortName="titv",required=true)
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@Input(doc="target Ti/Tv ratio for recalibration", shortName="titv", required=true)
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var target_titv: Float = _
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@Input(doc="downsampling coverage",shortName="dcov",required=false)
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@Input(doc="per-sample downsampling level",shortName="dcov",required=false)
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var downsampling_coverage = 300
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@Input(doc="Number of jobs to scatter UnifiedGenotyper",shortName="snpScatter",required=false)
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var num_snp_scatter_jobs = 50
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@Input(doc="level of parallelism for UnifiedGenotyper", shortName="snpScatter", required=false)
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var num_snp_scatter_jobs = 20
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@Input(doc="Number of jobs to scatter IndelGenotyperV2",shortName="indelScatter",required=false)
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@Input(doc="level of parallelism for IndelGenotyperV2", shortName="indelScatter", required=false)
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var num_indel_scatter_jobs = 5
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@Input(doc="Indel-clean BAM files",shortName="clean",required=false)
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var clean_bam_files = 1
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@Input(doc="Skip indel-cleaning for BAM files (for testing only)", shortName="skipCleaning", required=false)
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var skip_cleaning = false
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@Input(doc="ADPR script")
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var adprScript: File = _
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//@Input(doc="ADPR script")
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//var adprScript: File = _
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@Input(doc="Sequencing maching name (for use by adpr)")
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var machine: String = _
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//@Input(doc="Sequencing maching name (for use by adpr)")
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//var machine: String = _
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@Input(doc="Sequencing experiement type (for use by adpr)--Whole_Exome, Whole_Genome, or Hybrid_Selection")
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var protocol: String = _
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//@Input(doc="Sequencing experiement type (for use by adpr)--Whole_Exome, Whole_Genome, or Hybrid_Selection")
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//var protocol: String = _
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private var pipeline: Pipeline = _
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@ -80,16 +69,23 @@ class fullCallingPipeline extends QScript {
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def script = {
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pipeline = YamlUtils.load(classOf[Pipeline], qscript.pipelineYamlFile)
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pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile)
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val projectBase: String = qscript.pipeline.getProject.getName
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val cleanedBase: String = projectBase + ".cleaned"
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val uncleanedBase: String = projectBase + ".uncleaned"
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// there are commands that use all the bam files
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val recalibratedSamples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains("recalibrated"))
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val adprRScript = qscript.adprScript
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val seq = qscript.machine
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val expKind = qscript.protocol
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//val adprRScript = qscript.adprScript
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//val seq = qscript.machine
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//val expKind = qscript.protocol
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// count number of contigs (needed for indel cleaning parallelism)
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var contigCount = 0
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for ( line <- scala.io.Source.fromFile(qscript.contigIntervals).getLines ) {
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contigCount += 1
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}
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for ( sample <- recalibratedSamples ) {
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// put unclean bams in unclean genotypers in advance, create the extension files
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@ -112,7 +108,7 @@ class fullCallingPipeline extends QScript {
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realigner.input_file = targetCreator.input_file
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realigner.intervals = qscript.contigIntervals
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realigner.targetIntervals = new java.io.File(targetCreator.out.getAbsolutePath)
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realigner.scatterCount = qscript.numContigs
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realigner.scatterCount = contigCount
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// may need to explicitly run fix mates
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var fixMates = new PicardBamJarFunction {
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@ -157,8 +153,7 @@ class fullCallingPipeline extends QScript {
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samtoolsindex.bamFile = cleaned_bam
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samtoolsindex.analysisName = "index_"+cleaned_bam.getName
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// COMMENT THIS NEXT BLOCK TO SKIP CLEANING
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if (qscript.clean_bam_files == 1) {
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if (!qscript.skip_cleaning) {
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if ( realigner.scatterCount > 1 ) {
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add(targetCreator,realigner,samtoolsindex)
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} else {
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@ -177,18 +172,17 @@ class fullCallingPipeline extends QScript {
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.toList
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// actually make calls
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if (qscript.clean_bam_files == 1) {
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// COMMENT THIS NEXT LINE TO AVOID CALLING ON CLEANED FILES
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if (!qscript.skip_cleaning) {
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//endToEnd(cleanedBase, cleanBamFiles, adprRscript, seq, expKind)
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endToEnd(cleanedBase, cleanBamFiles, seq, expKind)
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endToEnd(cleanedBase, cleanBamFiles)
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} else {
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//endToEnd(uncleanedBase, recalibratedBamFiles, adprRscript, seq, expKind)
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endToEnd(uncleanedBase, recalibratedBamFiles, seq, expKind)
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endToEnd(uncleanedBase, recalibratedBamFiles)
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}
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}
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//def endToEnd(base: String, bamFiles: List[File], adprthing: File, seqinfo: String, exptype: String) = {
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def endToEnd(base: String, bamFiles: List[File], seqinfo: String, exptype: String) = {
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def endToEnd(base: String, bamFiles: List[File]) = {
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// step through the un-indel-cleaned graph:
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// 1a. call snps and indels
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@ -211,9 +205,9 @@ class fullCallingPipeline extends QScript {
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}
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// todo -- add generalize comp inputs
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if ( qscript.comp1KGCEU != null ) {
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snps.rodBind :+= RodBind( "comp1KG_CEU", "VCF", qscript.comp1KGCEU )
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}
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//if ( qscript.comp1KGCEU != null ) {
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// snps.rodBind :+= RodBind( "comp1KG_CEU", "VCF", qscript.comp1KGCEU )
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//}
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snps.scatterCount = qscript.num_snp_scatter_jobs
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@ -263,8 +257,8 @@ class fullCallingPipeline extends QScript {
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masker.variantVCF = annotated.out
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masker.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
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masker.maskName = "NearIndel"
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masker.clusterWindowSize = Some(qscript.snpClusterWindow)
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masker.clusterSize = Some(qscript.snpsInCluster)
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masker.clusterWindowSize = Some(10)
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masker.clusterSize = Some(3)
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masker.out = swapExt(annotated.out,".vcf",".indel.masked.vcf")
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masker.analysisName = base+"_Cluster_and_Indel_filter"
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