From 73c9adace2ec9e831983a591d151af477fc0d30a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 5 Jan 2021 16:23:58 -0600
Subject: [PATCH] Fix fail pre execution run
---
workflow/rna-seq.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d29490e..a05eaee 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -2121,13 +2121,13 @@ process failPreExecutionRun {
echo \${exist} >> ${repRID}.failPreExecutionRun.log
if [ "\${exist}" == "[]" ]
then
- rid=\$(python3 ${script_uploadExecutionRun_failPreExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d \${errorDetails} -o ${source} -c \${cookie} -u F)
+ rid=\$(python3 ${script_uploadExecutionRun_failPreExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${errorDetails}" -o ${source} -c \${cookie} -u F)
echo LOG: execution run RID uploaded - \${executionRun_rid} >> ${repRID}.failPreExecutionRun.log
else
rid=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
rid=\${rid:7:-6}
echo \${rid} >> ${repRID}.failPreExecutionRun.log
- executionRun_rid==\$(python3 ${script_uploadExecutionRun_failPreExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d \${errorDetails} -o ${source} -c \${cookie} -u \${rid})
+ executionRun_rid==\$(python3 ${script_uploadExecutionRun_failPreExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${errorDetails}" -o ${source} -c \${cookie} -u \${rid})
echo LOG: execution run RID updated - \${executionRun_rid} >> ${repRID}.failPreExecutionRun.log
fi
"""
@@ -2210,7 +2210,7 @@ process failExecutionRun {
pipelineError_details=\$(echo \${pipelineError_details}"|Species|${speciesMeta}|${speciesInfer}|\\n")
fi
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})
+ 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}.failExecutionRun.log
fi
"""
--
GitLab