Replace string \n with newline character

workflow/rna-seq.nf

@@ -1979,8 +1979,8 @@ process failExecutionRun {
   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 \${pipelineError_details}"|Metadata|Submitted value|Inferred value|\\n ")
+    pipelineError_details=\$(echo "**Submitted metadata does not match infered:**\\n")
+    pipelineError_details=\$(echo \${pipelineError_details}"|Metadata|Submitted value|Inferred value|\\n")
     pipelineError_details=\$(echo \${pipelineError_details}"|:-:|-:|-:|\\n")
     if ${pipelineError_ends}
     then
@@ -2003,22 +2003,22 @@ process failExecutionRun {
         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 ")
+      pipelineError_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 = \\"${strandedInfer}\\". ")
-      pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${strandedMeta}|${strandedInfer}|\\n ")
+      pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${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}|${spikeInfer}|\\n ")
+      pipelineError_details=\$(echo \${pipelineError_details}"|*Used_Spike_Ins*|${spikeMeta}|${spikeInfer}|\\n")
     fi
     if ${pipelineError_species}
     then
       #pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \\"${speciesMeta}\\" while inferred value = \\"${speciesInfer}\\". ")
-      pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|${speciesInfer}|\\n ")
+      pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|${speciesInfer}|\\n")
     fi
     #pipelineError_details=\$(echo "\${pipelineError_details::-1}")
     rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${pipelineError_details}" -o ${source} -c \${cookie} -u ${executionRunRID})

workflow/scripts/upload_execution_run.py

@@ -31,7 +31,7 @@ def main(hostname, catalog_number, credential):
             "Input_Bag": args.inputBagRID,
             "Notes": args.notes,
             "Execution_Status": args.status,
-            "Execution_Status_Detail": args.statusDetail
+            "Execution_Status_Detail": args.statusDetail.replace('\\n','\n')
         }
         entities = run_table.insert([run_data])
         rid = entities[0]["RID"]