From 475ad1259db518594b0801e8fa44b14b9a52e753 Mon Sep 17 00:00:00 2001 From: kshakir Date: Thu, 14 Apr 2011 02:22:31 +0000 Subject: [PATCH] Put a band-aid on the FCP by switching use of DINDEL to INDEL and explicitly running UG the old way with just indels and just snps. Switched YAML parser to new Broad parser which will additionally update picard cleaned bams to the latest version if the project and sample are specified. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5634 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/playground/FullCallingPipeline.q | 9 +++++---- .../playground/MultiFullCallingPipelineTest.scala | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/scala/qscript/playground/FullCallingPipeline.q b/scala/qscript/playground/FullCallingPipeline.q index 0c87e0c7a..bbf87c787 100755 --- a/scala/qscript/playground/FullCallingPipeline.q +++ b/scala/qscript/playground/FullCallingPipeline.q @@ -8,7 +8,7 @@ import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, Cl import org.broadinstitute.sting.queue.library.ipf.intervals.ExpandIntervals import org.broadinstitute.sting.queue.QScript import collection.JavaConversions._ -import org.broadinstitute.sting.utils.yaml.YamlUtils +import org.broadinstitute.sting.utils.broad.PicardPipeline class FullCallingPipeline extends QScript { qscript => @@ -49,8 +49,8 @@ class FullCallingPipeline extends QScript { // ------------ SETUP THE PIPELINE ----------- // - def script = { - pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile) + def script() { + pipeline = PicardPipeline.parse(qscript.yamlFile) val projectBase: String = qscript.pipeline.getProject.getName @@ -175,7 +175,7 @@ class FullCallingPipeline extends QScript { indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.indels.out") indels.memoryLimit = 6 indels.downsample_to_coverage = 600 - indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL + indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL indels.input_file = bamFiles indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp) indels.out = new File("IndelCalls", base+".indels.vcf") @@ -213,6 +213,7 @@ class FullCallingPipeline extends QScript { snps.memoryLimit = 6 snps.downsample_to_coverage = 600 snps.input_file = bamFiles + snps.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp) snps.out = new File("SnpCalls", base+".snps.vcf") diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala index d19b59d41..cccbe026e 100644 --- a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala +++ b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala @@ -54,7 +54,7 @@ class MultiFullCallingPipelineTest { final def convertDatasets: Array[Array[AnyRef]] = datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray - @Test(dataProvider="datasets", enabled=false) + @Test(dataProvider="datasets") def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) { val projectName = dataset.name val testName = "MultiFullCallingPipeline-" + projectName