From 6ff4315be7fb907df3d31b450ab5bf4c6c2a4e85 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 13 Sep 2020 11:10:28 -0500
Subject: [PATCH] Add datahub fetch for pipeline
---
workflow/rna-seq.nf | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b12b1f1..641ecda 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -415,6 +415,18 @@ process getRefInfer {
ln -s "\${references}"/bed ${refName}/bed
ln -s "\${references}"/genome.fna
ln -s "\${references}"/genome.gtf
+ elif [ ${referenceBase} == "dev.gudmap.org" ]
+ then
+ GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+ GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+ GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+ query=$(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 ${refURL})
+ if [ "${loc}" = "/hatrac/*" ]; then echo "LOG: Reference not present in hatrac"; exit 1; fi
+ filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+ deriva-hatrac-cli --host ${referenceBase} get ${refURL}
fi
echo -e "LOG: fetched" >> ${repRID}.${refName}.getRefInfer.log
@@ -729,6 +741,19 @@ process getRef {
ln -s "\${references}"/genome.gtf
ln -s "\${references}"/geneID.tsv
ln -s "\${references}"/Entrez.tsv
+ elif [ ${referenceBase} == "dev.gudmap.org" ]
+ then
+ GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+ GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+ GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+ query=$(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 ${refURL})
+ if [ "${loc}" = "/hatrac/*" ]; then echo "LOG: Reference not present in hatrac"; exit 1; fi
+ filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+ deriva-hatrac-cli --host ${referenceBase} get ${refURL}
+ fi
fi
echo -e "LOG: fetched" >> ${repRID}.getRef.log
"""
--
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