Add missing argument

Author: bbimber

singlecell/src/org/labkey/singlecell/run/CellBenderCiteSeqHandler.java

@@ -109,7 +109,8 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
 
             String exe = SequencePipelineService.get().getExeForPackage("CELLBENDERPATH", "cellbender").getPath();
             List<String> args = new ArrayList<>(Arrays.asList(
-                    exe, "--input", inputH5.getPath(),
+                    exe, "remove-background",
+                    "--input", inputH5.getPath(),
                     "--output", outputH5.getPath()
             ));
             args.addAll(getClientCommandArgs(ctx.getParams()));

singlecell/src/org/labkey/singlecell/run/CellBenderLoupeHandler.java

@@ -112,7 +112,8 @@ public File runCellBender(File input, JobContext ctx) throws PipelineJobExceptio
 
             String exe = SequencePipelineService.get().getExeForPackage("CELLBENDERPATH", "cellbender").getPath();
             List<String> args = new ArrayList<>(Arrays.asList(
-                    exe, "--input", inputH5.getPath(),
+                    exe, "remove-background",
+                    "--input", inputH5.getPath(),
                     "--output", outputH5.getPath()
             ));
             args.addAll(getClientCommandArgs(ctx.getParams()));