Update vireo args

bbimber · bbimber · commit 057d0276ffef · 2025-07-08T20:42:07.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
@@ -202,12 +202,6 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     cellsnp.add(maxThreads.toString());
                 }
 
-                cellsnp.add("--minMAF");
-                cellsnp.add("0.1");
-
-                cellsnp.add("--minCOUNT");
-                cellsnp.add("100");
-
                 String maxDepth = StringUtils.trimToNull(ctx.getParams().optString("maxDepth"));
                 if (maxDepth != null)
                 {
@@ -240,6 +234,12 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                         cellsnp.add("--chrom");
                         cellsnp.add(contigs);
                     }
+
+                    cellsnp.add("--minMAF");
+                    cellsnp.add("0.1");
+
+                    cellsnp.add("--minCOUNT");
+                    cellsnp.add("100");
                 }
 
                 new SimpleScriptWrapper(ctx.getLogger()).execute(cellsnp);

Original file line number	Diff line number	Diff line change
`@@ -202,12 +202,6 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`202`	`202`	`cellsnp.add(maxThreads.toString());`
`203`	`203`	`}`
`204`	`204`
`205`		`- cellsnp.add("--minMAF");`
`206`		`- cellsnp.add("0.1");`
`207`		`-`
`208`		`- cellsnp.add("--minCOUNT");`
`209`		`- cellsnp.add("100");`
`210`		`-`
`211`	`205`	`String maxDepth = StringUtils.trimToNull(ctx.getParams().optString("maxDepth"));`
`212`	`206`	`if (maxDepth != null)`
`213`	`207`	`{`
`@@ -240,6 +234,12 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`240`	`234`	`cellsnp.add("--chrom");`
`241`	`235`	`cellsnp.add(contigs);`
`242`	`236`	`}`
	`237`	`+`
	`238`	`+ cellsnp.add("--minMAF");`
	`239`	`+ cellsnp.add("0.1");`
	`240`	`+`
	`241`	`+ cellsnp.add("--minCOUNT");`
	`242`	`+ cellsnp.add("100");`
`243`	`243`	`}`
`244`	`244`
`245`	`245`	`new SimpleScriptWrapper(ctx.getLogger()).execute(cellsnp);`