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