Add validation to Cell Ranger steps

BimberLab · Aug 26, 2024 · 5330687 · 5330687
1 parent cb345c1
commit 5330687
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diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
@@ -483,6 +483,10 @@ public void complete(SequenceAnalysisJobSupport support, AnalysisModel model, Co
 
         File outsDir = outputForData.getFile().getParentFile();
         Integer dataId = outputForData.getDataId();
+        if (dataId == null)
+        {
+            throw new PipelineJobException("Unable to find dataId for output file");
+        }
 
         File metrics = new File(outsDir, "metrics_summary.csv");
         if (metrics.exists())

diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java
@@ -788,6 +788,10 @@ public void complete(SequenceAnalysisJobSupport support, AnalysisModel model, Co
 
             File outsDir = outputForData.getFile().getParentFile();
             Integer dataId = outputForData.getDataId();
+            if (dataId == null)
+            {
+                throw new PipelineJobException("Unable to find dataId for output file");
+            }
 
             addMetrics(outsDir, model, dataId);
         }