diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3ebe6e56b553448beae7398d89643a1511650999..3d1880a074452b9821d2203330f7ef0b2a9ff012 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -458,7 +458,7 @@ human_dev:
   - 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 ${refURL})
@@ -483,7 +483,7 @@ mouse_dev:
   - GRCv=$(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 ${refURL})
@@ -508,7 +508,7 @@ human_staging:
   - GRCv=$(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 ${refURL})
@@ -534,7 +534,7 @@ mouse_staging:
   - GRCv=$(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 ${refURL})
@@ -559,7 +559,7 @@ human_prod:
   - GRCv=$(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 ${refURL})
@@ -585,7 +585,7 @@ mouse_prod:
   - GRCv=$(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})