Allow nimble plot to run and not produce an HTML file

BimberLab · Jan 27, 2025 · fa50992 · fa50992
1 parent a569b46
commit fa50992
Showing 1 changed file with 3 additions and 11 deletions.
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -292,17 +292,9 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin
 
             output.addSequenceOutput(results, basename + ": nimble align", "Nimble Results", rs.getRowId(), null, genome.getGenomeId(), description);
 
+            // NOTE: situations like zero alignments would result in no report being created. Rely on the code in doAlign to verify proper execution of nimble
             File reportHtml = getReportHtmlFileFromResults(results);
-            if (!reportHtml.exists())
-            {
-                if (SequencePipelineService.get().hasMinLineCount(results, 2))
-                {
-                    long lineCount = SequencePipelineService.get().getLineCount(results);
-                    _ctx.getLogger().debug("Found {} lines in file {}", lineCount, results.getPath());
-                    throw new PipelineJobException("Unable to find file: " + reportHtml.getPath());
-                }
-            }
-            else
+            if (reportHtml.exists())
             {
                 output.addSequenceOutput(reportHtml, basename + ": nimble report", NIMBLE_REPORT_CATEGORY, rs.getRowId(), null, genome.getGenomeId(), description);
             }
@@ -554,7 +546,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt
 
             if (!plotResultsHtml.exists())
             {
-                throw new PipelineJobException("Missing file: " + plotResultsHtml.getPath());
+                ctx.getLogger().info("No report HTML generated, but nimble plot had exit code 0");
             }
         }
         else