Bugfix to GatherVcfsCloud

bbimber · bbimber · commit 551321d6804a · 2025-02-22T13:07:46.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GatherVcfsCloudWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GatherVcfsCloudWrapper.java
@@ -20,7 +20,7 @@ public GatherVcfsCloudWrapper(Logger log)
 
     public void gatherVcfs(File output, List<File> inputVcfs) throws PipelineJobException
     {
-        List<String> args = new ArrayList<>(getBaseArgs());
+        List<String> args = new ArrayList<>(getBaseArgs("GatherVcfsCloud"));
         args.add("-O");
         args.add(output.getPath());
 

Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,7 @@ public GatherVcfsCloudWrapper(Logger log)`
`20`	`20`
`21`	`21`	`public void gatherVcfs(File output, List<File> inputVcfs) throws PipelineJobException`
`22`	`22`	`{`
`23`		`- List<String> args = new ArrayList<>(getBaseArgs());`
	`23`	`+ List<String> args = new ArrayList<>(getBaseArgs("GatherVcfsCloud"));`
`24`	`24`	`args.add("-O");`
`25`	`25`	`args.add(output.getPath());`
`26`	`26`