Test fix

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java

@@ -23,11 +23,13 @@
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
+import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.TestContext;
@@ -111,7 +113,7 @@ public void testVariantProcessing() throws Exception
                 extraFiles.add(new File(job.getAnalysisDirectory(), jobName + "." + outputFileId + ".log"));
                 extraFiles.add(new File(job.getAnalysisDirectory(), "sequenceOutput.json"));
                 extraFiles.add(new File(job.getAnalysisDirectory(), "sequenceSupport.json.gz"));
-                extraFiles.add(new File(job.getAnalysisDirectory(), "gatk.ped"));
+                extraFiles.add(ProcessVariantsHandler.getPedigreeFile(job.getAnalysisDirectory(), "laboratory.subjects"));
                 extraFiles.add(new File(job.getAnalysisDirectory(), basename + ".gfiltered.selectVariants.annotated.filtered.vcf.gz"));
                 extraFiles.add(new File(job.getAnalysisDirectory(), basename + ".gfiltered.selectVariants.annotated.filtered.vcf.gz.tbi"));
                 extraFiles.add(new File(job.getAnalysisDirectory(), job.getBaseName() + ".pipe.xar.xml"));