From 296ee453c395cccc97b172b79d235910633c3cc5 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 14 Sep 2020 10:12:51 -0500
Subject: [PATCH] Fix ref move after getRef datahub pull
---
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 d493b75..d26b13c 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -783,6 +783,7 @@ process getRef {
# aws s3 cp "\${references}"/Entrez.tsv ./
elif [ ${referenceBase} == "dev.gudmap.org" ]
then
+ echo -e "LOG: grabbing reference files from datahub" >> ${repRID}.getRef.log
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)
@@ -796,8 +797,7 @@ process getRef {
filename=\$(echo \$(basename \${refURL}) | grep -oP '.*(?=:)')
deriva-hatrac-cli --host ${referenceBase} get \${refURL}
unzip \$(basename \${refURL})
- mv \${fName}/* .
- mv bed \${refName}/
+ mv \${fName}/data/* .
fi
echo -e "LOG: fetched" >> ${repRID}.getRef.log
"""
--
GitLab