From e0840868e02d1bbcbb4f02baf3e2fb78b4ab6c8f Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 3 Mar 2025 10:29:20 -0800
Subject: [PATCH] Correct argument

---
 singlecell/src/org/labkey/singlecell/run/NimbleHelper.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
index f26a336c7..c33ed37c4 100644
--- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
+++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -501,7 +501,7 @@ public static void write10xBarcodes(File bam, Logger log, Readset rs, ReferenceG
         // Write barcodes:
         DISCVRSeqRunner runner = new DISCVRSeqRunner(log);
         List<String> barcodeArgs = new ArrayList<>(runner.getBaseArgs("Save10xBarcodes"));
-        barcodeArgs.add("--bam");
+        barcodeArgs.add("-I");
         barcodeArgs.add(bam.getPath());
 
         File cbOutput = new File(bam.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(bam.getName()) + "cb.txt.gz");