From 9cccaef7d8b084dfb2e64a30b760027e81ee936c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 29 Jan 2021 12:54:49 -0600
Subject: [PATCH] Correct reference var name
---
workflow/rna-seq.nf | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index dbcfbc0..e3690bf 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1529,11 +1529,11 @@ process getRef {
# set the reference name
if [ "${species}" == "Mus musculus" ]
then
- references=\$(echo ${referenceBase}/GRCm${refMoVersion})
+ reference=\$(echo ${referenceBase}/GRCm${refMoVersion})
refName=GRCm
elif [ '${species}' == "Homo sapiens" ]
then
- references=\$(echo ${referenceBase}/GRCh${refHuVersion})
+ reference=\$(echo ${referenceBase}/GRCh${refHuVersion})
refName=GRCh
else
echo -e "LOG: ERROR - References could not be set!\nSpecies reference found: ${species}" >> ${repRID}.getRef.log
@@ -1541,12 +1541,12 @@ process getRef {
fi
if [ "${spike}" == "true" ]
then
- references=\$(echo \${reference}-S)
+ reference=\$(echo \${reference}-S)
elif [ "${spike}" == "false" ]
then
- reference=\$(echo \${references})
+ reference=\$(echo \${reference})
fi
- echo -e "LOG: species set to \${references}" >> ${repRID}.getRef.log
+ echo -e "LOG: species set to \${reference}" >> ${repRID}.getRef.log
# retreive appropriate reference appropriate location
echo -e "LOG: fetching ${species} reference files from ${referenceBase}" >> ${repRID}.getRef.log
@@ -1558,9 +1558,9 @@ process getRef {
elif [ arams.refSource == "datahub" ]
then
echo -e "LOG: grabbing reference files from datahub" >> ${repRID}.getRef.log
- GRCv=\$(echo \${references} | grep -o \${refName}.* | cut -d '.' -f1)
- GRCp=\$(echo \${references} | grep -o \${refName}.* | cut -d '.' -f2)
- GENCODE=\$(echo \${references} | grep -o \${refName}.* | cut -d '.' -f3)
+ GRCv=\$(echo \${reference} | grep -o \${refName}.* | cut -d '.' -f1)
+ GRCp=\$(echo \${reference} | grep -o \${refName}.* | cut -d '.' -f2)
+ GENCODE=\$(echo \${reference} | grep -o \${refName}.* | cut -d '.' -f3)
query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE})
curl --request GET \${query} > refQuery.json
refURL=\$(python ${script_refData} --returnParam URL)
--
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