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Commit 8a236b73 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix curl query

parent f0cf62ed
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2 merge requests!58Develop,!45Resolve "Move references to GUDMAP/RBK"
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workflow/rna-seq.nf
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......@@ -433,7 +433,7 @@ process getRefInfer {
GRCv=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f1)
GRCp=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f2)
GENCODE=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f3)
query=\$(echo 'https://'"${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})
curl --request GET \${query} > refQuery.json
refURL=\$(python ./workflow/scripts/extractRefData.py --returnParam URL)
loc=\$(dirname \${refURL})
......@@ -772,7 +772,7 @@ process getRef {
GRCv=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f1)
GRCp=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f2)
GENCODE=\$(echo \${references} | grep -o ${refName}.* | cut -d '.' -f3)
query=\$(echo 'https://'"${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})
curl --request GET \${query} > refQuery.json
refURL=\$(python ./workflow/scripts/extractRefData.py --returnParam URL)
loc=\$(dirname \${refURL})
......
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