Ensure nimble alignment file copied locally for docker

bbimber · bbimber · commit c2245926c48e · 2024-11-19T13:22:26.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java b/singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java
@@ -115,7 +115,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 }
 
                 // This will update these files in-place:
-                File alignmentFileLocal = NimbleHelper.ensureLocalCopy(alignmentFile);
+                File alignmentFileLocal = NimbleHelper.ensureLocalCopy(alignmentFile, output, ctx);
                 File reportFile = NimbleHelper.runNimbleReport(alignmentFileLocal, so.getLibrary_id(), output, ctx);
                 if (!reportFile.exists())
                 {

Original file line number	Diff line number	Diff line change
`@@ -115,7 +115,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`115`	`115`	`}`
`116`	`116`
`117`	`117`	`// This will update these files in-place:`
`118`		`- File alignmentFileLocal = NimbleHelper.ensureLocalCopy(alignmentFile);`
	`118`	`+ File alignmentFileLocal = NimbleHelper.ensureLocalCopy(alignmentFile, output, ctx);`
`119`	`119`	`File reportFile = NimbleHelper.runNimbleReport(alignmentFileLocal, so.getLibrary_id(), output, ctx);`
`120`	`120`	`if (!reportFile.exists())`
`121`	`121`	`{`