From 778044bcbdf996830a3958dbdc585292e33ba19c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 13 Sep 2020 23:05:07 -0500
Subject: [PATCH] Add search for ERCC ref
---
workflow/rna-seq.nf | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 01920de..e35317f 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -438,7 +438,12 @@ 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})
+ if [ "${refName}" != "ERCC" ]
+ then
+ query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='\${GRCv}'.'\${GRCp}'/Annotation_Version=GENCODE%20'\${GENCODE})
+ else
+ query=\$(echo 'https://${referenceBase}/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version=${refName}${refERCCVersion}/Annotation_Version=${refName}${refERCCVersion}')
+ fi
curl --request GET \${query} > refQuery.json
refURL=\$(python extractRefData.py --returnParam URL)
loc=\$(dirname \${refURL})
@@ -651,7 +656,6 @@ process inferMetadata {
elif [ 1 -eq \$(echo \$(expr \${percentR#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentF#*.} "<" 2500)) ]
then
stranded="reverse"
-
else
stranded="unstranded"
fi
--
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