From 9c845c6ea3685bb61fa31ffcc90070e436c15641 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 29 Oct 2019 16:40:38 -0500
Subject: [PATCH] Add back working deriva cookie copy (link)
---
workflow/rna-seq.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index fe52377..cb0ca67 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -8,7 +8,6 @@ params.outDir = "${baseDir}/../output"
// Parse input variables
deriva = file(params.deriva)
-deriva.copyTo('~/.bdbag/deriva-cookies.txt')
bdbag = Channel
.fromPath(params.bdbag)
.ifEmpty { exit 1, "bdbag zip file not found: ${params.bdbag}" }
@@ -35,6 +34,8 @@ process splitData {
"""
hostname
ulimit -a
+ ln -sf `readlink -e ${deriva}` ~/.bdbag/deriva-cookies.txt
+ echo LOG: deriva cookie linked
study=`echo "${bdbag}" | cut -d'.' -f1`
echo LOG: \${study}
unzip ${bdbag}
--
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