diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala index e6c6ead27..6eb1f4cd6 100644 --- a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala +++ b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala @@ -90,7 +90,7 @@ class FullCallingPipelineTest extends BaseTest { var cleanType = "cleaned" // Run the pipeline with the expected inputs. - var pipelineCommand = ("-retry 1 -S scala/qscript/fullCallingPipeline.q" + + var pipelineCommand = ("-retry 1 -S scala/qscript/playground/fullCallingPipeline.q" + " -jobProject %s -Y %s -refseqTable %s" + " --gatkjar %s/dist/GenomeAnalysisTK.jar") .format(projectName, yamlFile, dataset.refseq, new File(".").getAbsolutePath)