Update fail details

workflow/rna-seq.nf

@@ -1978,8 +1978,7 @@ process failExecutionRun {
     echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.finalizeExecutionRun.log
   elif [ ${pipelineError} == true ]
   then
-    #pipelineError_details=\$(echo "**Submitted metadata does not match infered:** ")
-    pipelineError_details=\$(echo "**Submitted metadata does not match infered:**\\n")
+    pipelineError_details=\$(echo "**Submitted metadata does not match inferred:**\\n")
     pipelineError_details=\$(echo \${pipelineError_details}"|Metadata|Submitted value|Inferred value|\\n")
     pipelineError_details=\$(echo \${pipelineError_details}"|:-:|-:|-:|\\n")
     if ${pipelineError_ends}
@@ -2001,26 +2000,21 @@ process failExecutionRun {
         endInfer="Paired End"
       else
         endInfer="unknown"
-      fi
-      #pipelineError_details=\$(echo \${pipelineError_details}"Paired_End: submitted value = \\""\${endMeta}"\\" while inferred value = \\""\${endInfer}"\\". ")
-      pipelineError_details=\$(echo \${pipelineError_details}"|*Paired_End*|"\${endMeta}"|"\${endInfer}"|\\n")
+      fipipelineError_details=\$(echo \${pipelineError_details}"|*Paired End*|"\${endMeta}"|"\${endInfer}"|\\n")
     fi
     if ${pipelineError_stranded}
-    then
-      #pipelineError_details=\$(echo \${pipelineError_details}"Strandedness: submitted value = \\"${strandedMeta}\\" while inferred value = \\"${strandedInfer}\\". ")
+    then#pipelineError_details=\$(echo \${pipelineError_details}"Strandedness: submitted value = \\"${strandedMeta}\\" while inferred value = \\"${strandedInfer}\\". ")
       pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${strandedMeta}|${strandedInfer}|\\n")
     fi
     if ${pipelineError_spike}
-    then
-      #pipelineError_details=\$(echo \${pipelineError_details}"Used_Spike_Ins: submitted value = \\"${spikeMeta}\\" while inferred value = \\"${spikeInfer}\\". ")
-      pipelineError_details=\$(echo \${pipelineError_details}"|*Used_Spike_Ins*|${spikeMeta}|${spikeInfer}|\\n")
+    then#pipelineError_details=\$(echo \${pipelineError_details}"Used_Spike_Ins: submitted value = \\"${spikeMeta}\\" while inferred value = \\"${spikeInfer}\\". ")
+      pipelineError_details=\$(echo \${pipelineError_details}"|*Used Spike Ins*|${spikeMeta}|${spikeInfer}|\\n")
     fi
     if ${pipelineError_species}
-    then
-      #pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \\"${speciesMeta}\\" while inferred value = \\"${speciesInfer}\\". ")
+    then#pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \\"${speciesMeta}\\" while inferred value = \\"${speciesInfer}\\". ")
       pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|${speciesInfer}|\\n")
     fi
-    #pipelineError_details=\$(echo "\${pipelineError_details::-1}")
+    pipelineError_details=\$(echo "\${pipelineError_details::-2}")
     rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${pipelineError_details}" -o ${source} -c \${cookie} -u ${executionRunRID})
     echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.finalizeExecutionRun.log
   fi