From d4099eb1cbb8c7319f1a8194daf0cfc2cf1d0704 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 19:48:47 -0600
Subject: [PATCH] Update fail details
---
workflow/rna-seq.nf | 20 +++++++-------------
1 file changed, 7 insertions(+), 13 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b124134..70c96da 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1978,8 +1978,7 @@ process failExecutionRun {
echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.finalizeExecutionRun.log
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 "**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}
@@ -2001,26 +2000,21 @@ process failExecutionRun {
endInfer="Paired End"
else
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")
+ 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 = \\"${strandedInfer}\\". ")
+ then#pipelineError_details=\$(echo \${pipelineError_details}"Strandedness: submitted value = \\"${strandedMeta}\\" while inferred value = \\"${strandedInfer}\\". ")
pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${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}|${spikeInfer}|\\n")
+ then#pipelineError_details=\$(echo \${pipelineError_details}"Used_Spike_Ins: submitted value = \\"${spikeMeta}\\" while inferred value = \\"${spikeInfer}\\". ")
+ pipelineError_details=\$(echo \${pipelineError_details}"|*Used Spike Ins*|${spikeMeta}|${spikeInfer}|\\n")
fi
if ${pipelineError_species}
- then
- #pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \\"${speciesMeta}\\" while inferred value = \\"${speciesInfer}\\". ")
+ then#pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \\"${speciesMeta}\\" while inferred value = \\"${speciesInfer}\\". ")
pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|${speciesInfer}|\\n")
fi
- #pipelineError_details=\$(echo "\${pipelineError_details::-1}")
+ pipelineError_details=\$(echo "\${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}.finalizeExecutionRun.log
fi
--
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