Missed with last commit

bbimber · bbimber · commit 66fb1d38be9a · 2024-11-15T15:54:35.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/DeepVariantHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/DeepVariantHandler.java
@@ -125,7 +125,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             }
 
             boolean retainVcf = ctx.getParams().optBoolean("retainVcf", false);
-            wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, retainVcf, ctx.getFileManager(), binVersion, args);
+            wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, retainVcf, ctx.getFileManager(), binVersion, args, ctx);
 
             action.addOutput(outputFile, "gVCF File", false);
 

Original file line number	Diff line number	Diff line change
`@@ -125,7 +125,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`125`	`125`	`}`
`126`	`126`
`127`	`127`	`boolean retainVcf = ctx.getParams().optBoolean("retainVcf", false);`
`128`		`- wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, retainVcf, ctx.getFileManager(), binVersion, args);`
	`128`	`+ wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, retainVcf, ctx.getFileManager(), binVersion, args, ctx);`
`129`	`129`
`130`	`130`	`action.addOutput(outputFile, "gVCF File", false);`
`131`	`131`