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A version of the full calling pipeline queue script that fully compiles without String/File/NamedFile type exceptions (e.g. expected String but got NamedFile/Expected NamedFile but got File). Pipeline itself is under testing with 5 bam files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4154 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-08-28 22:51:11 +00:00
parent 9c3f403307
commit 576ae30df1
1 changed files with 21 additions and 21 deletions
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42
scala/qscript/fullCallingPipeline.q
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@ -51,13 +51,13 @@ class fullCallingPipeline extends QScript {
@Input(doc="target titv for recalibration",shortName="titv",required=false)
var target_titv = 2.1
@Input(doc="downsampling coverage",shortname="dcov",required=false)
@Input(doc="downsampling coverage",shortName="dcov",required=false)
var downsampling_coverage = 200
@Input(doc="Number of jobs to scatter unifeid genotyper",shortname="snpScatter",required=false)
@Input(doc="Number of jobs to scatter unifeid genotyper",shortName="snpScatter",required=false)
var num_snp_scatter_jobs = 50
@Input(doc="Number of jobs to scatter indel genotyper",shortname="indelScatter",required=false)
@Input(doc="Number of jobs to scatter indel genotyper",shortName="indelScatter",required=false)
var num_indel_scatter_jobs = 5
@ -74,9 +74,9 @@ class fullCallingPipeline extends QScript {
val cleanedBase: String = projectBase + ".cleaned"
val uncleanedBase: String = projectBase + ".uncleaned"
// there are commands that use all the bam files
var cleanBamFiles = List.empty[File]
var cleanBamFiles = List.empty[NamedFile]
for ( bam <- bamFiles ) {
for ( bam <- qscript.bamFiles ) {
// put unclean bams in unclean genotypers
@ -88,7 +88,7 @@ class fullCallingPipeline extends QScript {
// create the cleaning commands
val targetCreator = new RealignerTargetCreator with CommandLineGATKArgs
targetCreator.input_file :+= bam
targetCreator.input_file :+= bam.toNamedFile
targetCreator.out = indel_targets
val realigner = new IndelRealigner with CommandLineGATKArgs
@ -103,17 +103,17 @@ class fullCallingPipeline extends QScript {
// put clean bams in clean genotypers
cleanBamFiles :+= realigner.out
cleanBamFiles :+= realigner.out.toNamedFile
add(targetCreator,realigner)
}
// actually make calls
endToEnd(uncleanedBase,bamFiles)
endToEnd(uncleanedBase,qscript.bamFiles)
endToEnd(cleanedBase,cleanBamFiles)
}
def endToEnd(base: String, bamFiles: List[File]) = {
def endToEnd(base: String, bamFiles: List[NamedFile]) = {
// step through the un-indel-cleaned graph:
// 1a. call snps and indels
@ -143,16 +143,16 @@ class fullCallingPipeline extends QScript {
// indel genotyper does one sample at a time
val indelCallFiles = List.empty[RodBind]
val indelGenotypers = List.empty[IndelGenotyperV2]
val loopNo = 0
val priority = ""
for ( bam <- bamFiles ) {
var indelCallFiles = List.empty[RodBind]
var indelGenotypers = List.empty[IndelGenotyperV2 with CommandLineGATKArgs]
var loopNo = 0
var priority = ""
for ( bam <- qscript.bamFiles ) {
val indel = new IndelGenotyperV2 with CommandLineGATKArgs
indel.input_file :+= bam
indel.input_file :+= bam.toNamedFile
indel.out = swapExt(bam,".bam",".indels.vcf")
indel.downsample_to_coverage = Some(500)
indelCallFiles :+= new RodBind("v"+loopNo.toString, "VCF", indel.out)
indelCallFiles :+= RodBind("v"+loopNo.toString, "VCF", indel.out)
indel.scatterCount = qscript.num_indel_scatter_jobs
indelGenotypers :+= indel
@ -165,10 +165,10 @@ class fullCallingPipeline extends QScript {
loopNo += 1
}
val mergeIndels = new CombineVariants with CommandLineGATKArgs
mergeIndels.out = qscript.project+".indels.vcf"
mergeIndels.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE
mergeIndels.out = new File(qscript.project+".indels.vcf")
mergeIndels.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)
mergeIndels.priority = priority
mergeIndels.variantmergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
mergeIndels.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
mergeIndels.rodBind = indelCallFiles
@ -185,7 +185,7 @@ class fullCallingPipeline extends QScript {
// 2.a filter on cluster and near indels
val masker = new VariantFiltration with CommandLineGATKArgs
masker.rodBind :+= RodBind("variant", "VCF", new File(annotated.vcfOutput))
masker.rodBind :+= RodBind("mask", "VCF", new File(mergeIndels.out))
masker.rodBind :+= RodBind("mask", "VCF", new File(mergeIndels.out.getAbsolutePath))
masker.maskName = "NearIndel"
masker.clusterWindowSize = Some(qscript.snpClusterWindow)
masker.clusterSize = Some(qscript.snpsInCluster)
@ -195,7 +195,7 @@ class fullCallingPipeline extends QScript {
// 2.b hand filter with standard filter
val handFilter = new VariantFiltration with CommandLineGATKArgs
handFilter.rodBind :+= RodBind("variant", "VCF", new File(annotated.vcfOutput))
handFilter.rodBind :+= RodBind("mask", "VCF", new File(indels.variants_out))
handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","QD<5","\"HRun>=4\"")
handFilter.out = swapExt(new File(annotated.vcfOutput),".vcf",".handfiltered.vcf")