Ensure nimble alignment file copied locally for docker

Author: bbimber

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

@@ -670,18 +670,23 @@ private static boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutpu
     }
 
     private File ensureLocalCopy(File input, PipelineStepOutput output) throws PipelineJobException
+    {
+        return ensureLocalCopy(input, output, getPipelineCtx());
+    }
+
+    public static File ensureLocalCopy(File input, PipelineStepOutput output, PipelineContext ctx) throws PipelineJobException
     {
         try
         {
-            if (getPipelineCtx().getWorkingDirectory().equals(input.getParentFile()))
+            if (ctx.getWorkingDirectory().equals(input.getParentFile()))
             {
                 return input;
             }
 
-            File local = new File(getPipelineCtx().getWorkingDirectory(), input.getName());
+            File local = new File(ctx.getWorkingDirectory(), input.getName());
             if (!local.exists())
             {
-                getPipelineCtx().getLogger().debug("Copying file locally: " + input.getPath());
+                ctx.getLogger().debug("Copying file locally: " + input.getPath());
                 FileUtils.copyFile(input, local);
             }
 

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

@@ -115,7 +115,8 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 }
 
                 // This will update these files in-place:
-                File reportFile = NimbleHelper.runNimbleReport(alignmentFile, so.getLibrary_id(), output, ctx);
+                File alignmentFileLocal = NimbleHelper.ensureLocalCopy(alignmentFile);
+                File reportFile = NimbleHelper.runNimbleReport(alignmentFileLocal, so.getLibrary_id(), output, ctx);
                 if (!reportFile.exists())
                 {
                     throw new PipelineJobException("Unable to find file: " + reportFile.getPath());