From 1cf16a8ff154a4aa623bdcd81a99349668a28f0a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 19:01:01 -0600
Subject: [PATCH] Add double excape to new line in fail
---
workflow/rna-seq.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b622e04..a262cdd 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -2002,22 +2002,22 @@ process failExecutionRun {
endInfer="unknown"
fi
pipelineError_details=\$(echo \${pipelineError_details}"Paired_End: submitted value = \""\${endMeta}"\" while inferred value = \""\${endsInfer}"\". ")
- #pipelineError_details=\$(echo \${pipelineError_details}"|*Paired_End*|"\${endMeta}"|"\${endsInfer}"|\n ")
+ #pipelineError_details=\$(echo \${pipelineError_details}"|*Paired_End*|"\${endMeta}"|"\${endsInfer}"|\\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})
--
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