From 8a236b737e0cb02ff77e460e797a06c00865f9dc Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 13 Sep 2020 20:55:14 -0500
Subject: [PATCH] Fix curl query
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d6a2bb0..41e11c7 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -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})
--
GitLab