From 9d37cf2aac216505f411cb4a9b696aa03e93709f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 10 Feb 2021 15:20:40 -0600
Subject: [PATCH] Fix datahub ref download
---
workflow/rna-seq.nf | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 555f711..264da73 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -790,20 +790,20 @@ process getRefInfer {
# retreive appropriate reference appropriate location
echo -e "LOG: fetching ${refName} reference files from ${referenceBase}" >> ${repRID}.${refName}.getRefInfer.log
- if [ ${referenceBase} == "/project/BICF/BICF_Core/shared/gudmap/references/new" ]
+ if [ "${referenceBase}" == "/project/BICF/BICF_Core/shared/gudmap/references/new" ]
then
unzip \${references}.zip
mv \$(basename \${references})/data/* .
- elif [ params.refSource == "datahub" ]
+ elif [ "${params.refSource}" == "datahub" ]
then
GRCv=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f1)
GRCp=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f2)
GENCODE=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f3)
if [ "${refName}" != "ERCC" ]
then
- query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE})
+ query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE}'/Used_Spike_Ins=false')
else
- query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${refName}${refERCCVersion}/Annotation_Version=${refName}${refERCCVersion}')
+ query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${refName}${refERCCVersion}'/Annotation_Version='${refName}${refERCCVersion}'/Used_Spike_Ins=false')
fi
curl --request GET \${query} > refQuery.json
refURL=\$(python ${script_refDataInfer} --returnParam URL)
@@ -1555,13 +1555,18 @@ process getRef {
echo -e "LOG: grabbing reference files from local (BioHPC)" >> ${repRID}.getRef.log
unzip \${reference}.zip
mv \$(basename \${reference})/data/* .
- elif [ arams.refSource == "datahub" ]
+ elif [ ${params.refSource} == "datahub" ]
then
echo -e "LOG: grabbing reference files from datahub" >> ${repRID}.getRef.log
GRCv=\$(echo \${reference} | grep -o \${refName}.* | cut -d '.' -f1)
GRCp=\$(echo \${reference} | grep -o \${refName}.* | cut -d '.' -f2)
GENCODE=\$(echo \${reference} | grep -o \${refName}.* | cut -d '.' -f3)
- query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE})
+ if [ "${spike}" == "true" ]
+ then
+ query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE}'/Used_Spike_Ins=true')
+ else
+ query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE}'/Used_Spike_Ins=false')
+ fi
curl --request GET \${query} > refQuery.json
refURL=\$(python ${script_refData} --returnParam URL)
loc=\$(dirname \${refURL})
--
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