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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3902 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
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.QScript
import org.broadinstitute.sting.queue.QScript._
// 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
/////////////////////////////////////////////////
// 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])
@Output(doc="Realigner targets")
var realignerIntervals: File = _
@ -36,7 +41,7 @@ class RealignerTargetCreator extends GatkFunction {
// 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")
var intervalsToClean: File = _
@Scatter(classOf[ContigScatterFunction])
@ -55,7 +60,7 @@ class IndelRealigner extends GatkFunction {
// 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)
var trigger: File = _
@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
/////////////////////////////////////////////////
class UnifiedGenotyperIndels extends GatkFunction {
class UnifiedGenotyperIndels extends GatkFunctionLocal {
@Gather(classOf[SimpleTextGatherFunction])
@Output(doc="indel vcf")
var indelVCF: File = _
@ -99,7 +104,7 @@ class UnifiedGenotyperIndels extends GatkFunction {
/////////////////////////////////////////////////
// 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")
var unfilteredVCF: File = _
@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
/////////////////////////////////////////////////
class GenerateVariantClusters extends GatkFunction {
class GenerateVariantClusters extends GatkFunctionLocal {
@Input(doc="A VCF that has been filtered for clusters and indels")
var initialFilteredVCF: File = _
@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
/////////////////////////////////////////////////
class ApplyGaussianClusters extends GatkFunction {
class ApplyGaussianClusters extends GatkFunctionLocal {
@Input(doc="A VCF file to which to apply clusters")
var inputVCF: 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
/////////////////////////////////////////////////
class ApplyVariantCuts extends GatkFunction {
class ApplyVariantCuts extends GatkFunctionLocal {
@Input(doc="A VCF file that has been recalibrated")
var recalibratedVCF: File = _
@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]
/////////////////////////////////////////////////
class GenomicAnnotator extends GatkFunction {
class GenomicAnnotator extends GatkFunctionLocal {
@Input(doc="A VCF file to be annotated")
var inputVCF: File = _
@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
/////////////////////////////////////////////////
class VariantEval extends GatkFunction {
class VariantEval extends GatkFunctionLocal {
@Input(doc="An optimized vcf file to evaluate")
var optimizedVCF: File = _
@Input(doc="A hand-fitlered vcf file to evaluate")