Reset job errors before submitting to the cluster

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java

@@ -721,7 +721,7 @@ private void runSnpEff(JobContext ctx, Map<String, SiteAndAlleles> siteToAllele,
             }
 
             File snpEffBaseDir = SNPEffStep.checkOrCreateIndex(ctx.getSequenceSupport(), ctx.getLogger(), genome, geneFileId);
-            File outputVcfSnpEff = new File(ctx.getOutputDir(), basename + ".snpeff.vcf.gz");
+            File outputVcfSnpEff = new File(ctx.getOutputDir(), basename + "snpeff.vcf.gz");
             snpEffWrapper.runSnpEff(genome.getGenomeId(), geneFileId, snpEffBaseDir, vcfOut, outputVcfSnpEff, null);
         }
     }

cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java

@@ -373,6 +373,10 @@ else if (j.getClusterId() == null)
     private boolean doSubmitJobToCluster(ClusterJob j, PipelineJob job) throws PipelineJobException
     {
         boolean success = false;
+
+        //NOTE: clear errors, since a previously failed/retried job will have non-zero errors
+        job.setErrors(0);
+
         List<String> ret = submitJobToCluster(j, job);
         if (j.getClusterId() != null)
         {