Change order of steps when no BAM present

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAnalysisTask.java

@@ -365,6 +365,18 @@ private void processAnalyses(AnalysisModelImpl analysisModel, int runId, List<Re
             getJob().getLogger().info("no analyses were selected");
         }
 
+        getJob().getLogger().info("creating analysis record");
+        TableInfo ti = SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_ANALYSES);
+        if (analysisModel.getRowId() == null)
+        {
+            analysisModel = Table.insert(getJob().getUser(), ti, analysisModel);
+            getJob().getLogger().info("created analysis: " + analysisModel.getRowId());
+        }
+        else
+        {
+            getJob().getLogger().info("re-using existing analysis: " + analysisModel.getRowId());
+        }
+
         File bam = analysisModel.getAlignmentFile() == null ? null : ExperimentService.get().getExpData(analysisModel.getAlignmentFile()).getFile();
         if (bam == null)
         {
@@ -379,18 +391,6 @@ private void processAnalyses(AnalysisModelImpl analysisModel, int runId, List<Re
             return;
         }
 
-        getJob().getLogger().info("creating analysis record for BAM: " + bam.getName());
-        TableInfo ti = SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_ANALYSES);
-        if (analysisModel.getRowId() == null)
-        {
-            analysisModel = Table.insert(getJob().getUser(), ti, analysisModel);
-            getJob().getLogger().info("created analysis: " + analysisModel.getRowId());
-        }
-        else
-        {
-            getJob().getLogger().info("re-using existing analysis: " + analysisModel.getRowId());
-        }
-
         if (!discardBam)
         {
             ExpData d = ExperimentService.get().getExpDataByURL(bam, getJob().getContainer());

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

@@ -488,6 +488,11 @@ public void complete(SequenceAnalysisJobSupport support, AnalysisModel model, Co
             throw new PipelineJobException("Unable to find dataId for output file");
         }
 
+        if (model.getRowId() == null)
+        {
+            throw new PipelineJobException("Unable to find rowId for analysis");
+        }
+
         File metrics = new File(outsDir, "metrics_summary.csv");
         if (metrics.exists())
         {