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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3902 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2010-07-29 20:48:35 +00:00
parent ba1a330293
commit 0f9baa2e94
1 changed files with 15 additions and 10 deletions
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25
scala/qscript/fullCallingPipeline.q
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@ -1,4 +1,5 @@
import org.broadinstitute.sting.queue.function.scattergather.{ContigScatterFunction, FixMatesGatherFunction} import org.broadinstitute.sting.queue.function.scattergather.{ContigScatterFunction, FixMatesGatherFunction}
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.QScript._ import org.broadinstitute.sting.queue.QScript._
// Other imports can be added here // Other imports can be added here
@ -23,8 +24,12 @@ def parseArgs(flag: String): String = {
///////////////////////////////////////////////// /////////////////////////////////////////////////
// step one: we need to create a set of realigner targets, one for each bam file // step one: we need to create a set of realigner targets, one for each bam file
///////////////////////////////////////////////// /////////////////////////////////////////////////
// todo -- make me less of a hack that makes Khalid cry
abstract class GatkFunctionLocal extends GatkFunction {
this.intervals = QScript.inputs("interval_list").head
}
class RealignerTargetCreator extends GatkFunction { class RealignerTargetCreator extends GatkFunctionLocal {
@Gather(classOf[SimpleTextGatherFunction]) @Gather(classOf[SimpleTextGatherFunction])
@Output(doc="Realigner targets") @Output(doc="Realigner targets")
var realignerIntervals: File = _ var realignerIntervals: File = _
@ -36,7 +41,7 @@ class RealignerTargetCreator extends GatkFunction {
// step two: we need to clean each bam file - gather will fix mates // step two: we need to clean each bam file - gather will fix mates
///////////////////////////////////////////////// /////////////////////////////////////////////////
class IndelRealigner extends GatkFunction { class IndelRealigner extends GatkFunctionLocal {
@Input(doc="Intervals to clean") @Input(doc="Intervals to clean")
var intervalsToClean: File = _ var intervalsToClean: File = _
@Scatter(classOf[ContigScatterFunction]) @Scatter(classOf[ContigScatterFunction])
@ -55,7 +60,7 @@ class IndelRealigner extends GatkFunction {
// step three: we need to call (multisample) over all bam files // step three: we need to call (multisample) over all bam files
///////////////////////////////////////////////// /////////////////////////////////////////////////
class UnifiedGenotyper extends GatkFunction { class UnifiedGenotyper extends GatkFunctionLocal {
@Input(doc="An optional trigger track (trigger emit will be set to 0)",required=false) @Input(doc="An optional trigger track (trigger emit will be set to 0)",required=false)
var trigger: File = _ var trigger: File = _
@Input(doc="A list of comparison files for annotation",required=false) @Input(doc="A list of comparison files for annotation",required=false)
@ -87,7 +92,7 @@ class UnifiedGenotyper extends GatkFunction {
// step four: we need to call indels (multisample) over all bam files // step four: we need to call indels (multisample) over all bam files
///////////////////////////////////////////////// /////////////////////////////////////////////////
class UnifiedGenotyperIndels extends GatkFunction { class UnifiedGenotyperIndels extends GatkFunctionLocal {
@Gather(classOf[SimpleTextGatherFunction]) @Gather(classOf[SimpleTextGatherFunction])
@Output(doc="indel vcf") @Output(doc="indel vcf")
var indelVCF: File = _ var indelVCF: File = _
@ -99,7 +104,7 @@ class UnifiedGenotyperIndels extends GatkFunction {
///////////////////////////////////////////////// /////////////////////////////////////////////////
// step five: we need to filter variants on cluster and with indel mask // step five: we need to filter variants on cluster and with indel mask
///////////////////////////////////////////////// /////////////////////////////////////////////////
class VariantFiltration extends GatkFunction { class VariantFiltration extends GatkFunctionLocal {
@Input(doc="A VCF file to filter") @Input(doc="A VCF file to filter")
var unfilteredVCF: File = _ var unfilteredVCF: File = _
@Input(doc="An interval mask to use to filter indels") @Input(doc="An interval mask to use to filter indels")
@ -119,7 +124,7 @@ class VariantFiltration extends GatkFunction {
///////////////////////////////////////////////// /////////////////////////////////////////////////
// step six: we need to generate gaussian clusters with the optimizer // step six: we need to generate gaussian clusters with the optimizer
///////////////////////////////////////////////// /////////////////////////////////////////////////
class GenerateVariantClusters extends GatkFunction { class GenerateVariantClusters extends GatkFunctionLocal {
@Input(doc="A VCF that has been filtered for clusters and indels") @Input(doc="A VCF that has been filtered for clusters and indels")
var initialFilteredVCF: File = _ var initialFilteredVCF: File = _
@Output(doc="Variant cluster file generated from input VCF") @Output(doc="Variant cluster file generated from input VCF")
@ -141,7 +146,7 @@ class GenerateVariantClusters extends GatkFunction {
///////////////////////////////////////////////// /////////////////////////////////////////////////
// step seven: we need to apply gaussian clusters to our variants // step seven: we need to apply gaussian clusters to our variants
///////////////////////////////////////////////// /////////////////////////////////////////////////
class ApplyGaussianClusters extends GatkFunction { class ApplyGaussianClusters extends GatkFunctionLocal {
@Input(doc="A VCF file to which to apply clusters") @Input(doc="A VCF file to which to apply clusters")
var inputVCF: File = _ var inputVCF: File = _
@Input(doc="A variant cluster file") @Input(doc="A variant cluster file")
@ -157,7 +162,7 @@ class ApplyGaussianClusters extends GatkFunction {
///////////////////////////////////////////////// /////////////////////////////////////////////////
// step eight: we need to make tranches out of the recalibrated qualities // step eight: we need to make tranches out of the recalibrated qualities
///////////////////////////////////////////////// /////////////////////////////////////////////////
class ApplyVariantCuts extends GatkFunction { class ApplyVariantCuts extends GatkFunctionLocal {
@Input(doc="A VCF file that has been recalibrated") @Input(doc="A VCF file that has been recalibrated")
var recalibratedVCF: File = _ var recalibratedVCF: File = _
@Output(doc="A VCF file that has had tranches marked") @Output(doc="A VCF file that has had tranches marked")
@ -173,7 +178,7 @@ class ApplyVariantCuts extends GatkFunction {
///////////////////////////////////////////////// /////////////////////////////////////////////////
// step nine: we need to annotate variants using the annotator [or maf, for now] // step nine: we need to annotate variants using the annotator [or maf, for now]
///////////////////////////////////////////////// /////////////////////////////////////////////////
class GenomicAnnotator extends GatkFunction { class GenomicAnnotator extends GatkFunctionLocal {
@Input(doc="A VCF file to be annotated") @Input(doc="A VCF file to be annotated")
var inputVCF: File = _ var inputVCF: File = _
@Input(doc="Refseq input table to use with the annotator") @Input(doc="Refseq input table to use with the annotator")
@ -190,7 +195,7 @@ class GenomicAnnotator extends GatkFunction {
///////////////////////////////////////////////// /////////////////////////////////////////////////
// step ten: we need to evaluate variants with variant eval // step ten: we need to evaluate variants with variant eval
///////////////////////////////////////////////// /////////////////////////////////////////////////
class VariantEval extends GatkFunction { class VariantEval extends GatkFunctionLocal {
@Input(doc="An optimized vcf file to evaluate") @Input(doc="An optimized vcf file to evaluate")
var optimizedVCF: File = _ var optimizedVCF: File = _
@Input(doc="A hand-fitlered vcf file to evaluate") @Input(doc="A hand-fitlered vcf file to evaluate")