From b7d88e9e98ef4e0d4628687310a9c884d85d3361 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 20:02:19 -0600
Subject: [PATCH] Remove italics from meta
---
workflow/rna-seq.nf | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 70c96da..5f13a4e 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -2000,21 +2000,21 @@ process failExecutionRun {
endInfer="Paired End"
else
endInfer="unknown"
- fipipelineError_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 = \\"${strandedInfer}\\". ")
- pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${strandedMeta}|${strandedInfer}|\\n")
+ then
+ pipelineError_details=\$(echo \${pipelineError_details}"|Strandedness|${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}|${spikeInfer}|\\n")
+ then
+ pipelineError_details=\$(echo \${pipelineError_details}"|Used Spike Ins|${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}|${speciesInfer}|\\n")
+ then
+ pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n")
fi
- pipelineError_details=\$(echo "\${pipelineError_details::-2}")
+ #ipelineError_details=\$(echo "\${pipelineError_details::-}")
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
--
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