From 375d8cad429988e34215dc51a56886e02714f778 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 20:13:52 -0600
Subject: [PATCH] Fix fail
---
workflow/rna-seq.nf | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 70043b7..7cfff2c 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -2000,7 +2000,8 @@ process failExecutionRun {
endInfer="Paired End"
else
endInfer="unknown"
- fipipelineError_details=\$(echo \${pipelineError_details}"|Paired End|"\${endMeta}"|"\${endInfer}"|\\n")
+ fi
+ pipelineError_details=\$(echo \${pipelineError_details}"|Paired End|"\${endMeta}"|"\${endInfer}"|\\n")
fi
if ${pipelineError_stranded}
then
@@ -2014,7 +2015,7 @@ process failExecutionRun {
then
pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n")
fi
- #pipelineError_details=\${pipelineError_details::-2}
+ pipelineError_details=\${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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