Bugfix to NimbleAlignmentStep

bbimber · bbimber · commit 600cda3b07a3 · 2025-10-16T19:02:17.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java b/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java
@@ -140,7 +140,7 @@ private File getCachedBarcodeFile(Readset rs, boolean throwIfNotFound) throws Pi
 
     private File getUmiMapping(File cellbarcodeFile) throws PipelineJobException
     {
-        File ret = new File(cellbarcodeFile.getPath().replaceAll(".cb.txt.gz", ".umi.txt.gz"));
+        File ret = new File(cellbarcodeFile.getPath().replaceAll("cb.txt.gz", "umi.txt.gz"));
         if (ret == null || ! ret.exists())
         {
             throw new PipelineJobException("Missing cached UMI file: " + ret.getPath());

Original file line number	Diff line number	Diff line change
`@@ -140,7 +140,7 @@ private File getCachedBarcodeFile(Readset rs, boolean throwIfNotFound) throws Pi`
`140`	`140`
`141`	`141`	`private File getUmiMapping(File cellbarcodeFile) throws PipelineJobException`
`142`	`142`	`{`
`143`		`- File ret = new File(cellbarcodeFile.getPath().replaceAll(".cb.txt.gz", ".umi.txt.gz"));`
	`143`	`+ File ret = new File(cellbarcodeFile.getPath().replaceAll("cb.txt.gz", "umi.txt.gz"));`
`144`	`144`	`if (ret == null \|\| ! ret.exists())`
`145`	`145`	`{`
`146`	`146`	`throw new PipelineJobException("Missing cached UMI file: " + ret.getPath());`