From 525b8bd9154ac17c203c56f8309d48decb2ecb82 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 20:56:30 -0600
Subject: [PATCH] Fix extra quotes in pares
---
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 f1334a3..b803670 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -344,7 +344,7 @@ process parseMetadata {
# get read length metadata
readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p readLength)
- if [ "\${readLength}" = "nan"]
+ if [ "\${readLength}" = "nan" ]
then
readLength="NA"
fi
@@ -357,11 +357,11 @@ process parseMetadata {
then
fastqCountError=true
fastqCountError_details="Too many fastqs detected (>2)"
- elif [ "\${endsMeta}"" == "se" ] && [ "${fastqCount}" -ne "1" ]
+ elif [ "\${endsMeta}" == "se" ] && [ "${fastqCount}" -ne "1" ]
then
fastqCountError=true
fastqCountError_details="Number of fastqs detected does not match submitted endness"
- elif [ "\${endsMeta}"" == "pe" ] && [ "${fastqCount}" -ne "2" ]
+ elif [ "\${endsMeta}" == "pe" ] && [ "${fastqCount}" -ne "2" ]
then
fastqCountError=true
fastqCountError_details="Number of fastqs detected does not match submitted endness"
--
GitLab