From 06b4cad780abc52e5cd24cc7e0c3db9f39471ff5 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Mon, 4 Jan 2021 19:42:54 -0600 Subject: [PATCH] Replace string \n with newline character --- workflow/rna-seq.nf | 12 ++++++------ workflow/scripts/upload_execution_run.py | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 3da24e2..b124134 100644 --- a/workflow/rna-seq.nf +++ b/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}) diff --git a/workflow/scripts/upload_execution_run.py b/workflow/scripts/upload_execution_run.py index 5af8565..273dc5d 100644 --- a/workflow/scripts/upload_execution_run.py +++ b/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"] -- GitLab