Revert fail execution run

workflow/rna-seq.nf

@@ -2293,37 +2293,43 @@ process failExecutionRun {
   cookie=\${cookie:11:-1}
 
   errorDetails=""
-  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}
+  if [ ${pipelineError} == false ]
   then
-    if [ "${endsInfer}" == "se" ]
+    rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Success -d 'Run Successful' -o ${source} -c \${cookie} -u ${executionRunRID})
+    echo LOG: execution run RID marked as successful - \${rid} >> ${repRID}.failExecutionRun.log
+  else
+    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 ${pipelineError_ends}
     then
-      endInfer="Single End"
-    elif [ "${endsInfer}" == "pe" ]
+      if [ "${endsInfer}" == "se" ]
+      then
+        endInfer="Single End"
+      elif [ "${endsInfer}" == "pe" ]
+      then
+        endInfer="Paired End"
+      else
+        endInfer="unknown"
+      fi
+      pipelineError_details=\$(echo \${pipelineError_details}"|Paired End|${endsRaw}|"\${endInfer}"|\\n")
+    fi
+    if ${pipelineError_stranded}
     then
-      endInfer="Paired End"
-    else
-      endInfer="unknown"
+      pipelineError_details=\$(echo \${pipelineError_details}"|Strandedness|${strandedMeta}|${strandedInfer}|\\n")
     fi
-    pipelineError_details=\$(echo \${pipelineError_details}"|Paired End|${endsRaw}|"\${endInfer}"|\\n")
-  fi
-  if ${pipelineError_stranded}
-  then
-    pipelineError_details=\$(echo \${pipelineError_details}"|Strandedness|${strandedMeta}|${strandedInfer}|\\n")
-  fi
-  if ${pipelineError_spike}
-  then
-    pipelineError_details=\$(echo \${pipelineError_details}"|Used Spike Ins|${spikeMeta}|${spikeInfer}|\\n")
-  fi
-  if ${pipelineError_species}
-  then
-    pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n")
+    if ${pipelineError_spike}
+    then
+      pipelineError_details=\$(echo \${pipelineError_details}"|Used Spike Ins|${spikeMeta}|${spikeInfer}|\\n")
+    fi
+    if ${pipelineError_species}
+    then
+      pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n")
+    fi
+    pipelineError_details=\${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}.failExecutionRun.log
   fi
-  pipelineError_details=\${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}.failExecutionRun.log
   
   dt=`date --utc +%FT%TZ`
   curl -H 'Content-Type: application/json' -X PUT -d \