From c0e6c65923347869b315207a73f220fdb246916a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 13 Apr 2021 22:13:10 -0500
Subject: [PATCH] Fix failPreExecutionRun error collection
---
CHANGELOG.md | 1 +
rna-seq.nf | 10 +++++-----
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1feda59..a85a844 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,7 @@
* Add test for DNAnexus env
* Add test for AWS env
* Fix fetch fastq count
+* Fix failPreExecutionRun error collection
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
diff --git a/rna-seq.nf b/rna-seq.nf
index a1dcd02..e1a0777 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -2715,19 +2715,19 @@ process failPreExecutionRun {
errorDetails=""
if [ ${fastqCountError} == true ]
then
- errorDetails=\$(echo ${fastqCountError_details}"\\n")
+ errorDetails=\$(echo "${fastqCountError_details}"\\n")
elif [ ${fastqReadError} == true ]
then
- errorDetails=\$(echo \$(errorDetails)${fastqReadError_details}"\\n")
+ errorDetails=\$(echo "\${errorDetails}${fastqReadError_details}\\n")
elif [ ${fastqFileError} == true ]
then
- errorDetails=\$(echo \$(errorDetails)${fastqFileError_details}"\\n")
+ errorDetails=\$(echo "\${errorDetails}${fastqFileError_details}\\n")
elif [ ${seqtypeError} == true ]
then
- errorDetails=\$(echo \$(errorDetails)${seqtypeError_details}"\\n")
+ errorDetails=\$(echo "\${errorDetails}${seqtypeError_details}\\n")
elif [ ${speciesError} == true ]
then
- errorDetails=\$(echo \$(errorDetails)${speciesError_details}"\\n")
+ errorDetails=\$(echo "\${errorDetails}${speciesError_details}\\n")
fi
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log
--
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