From c02d977abd1a2ca4c4b7d1d5d5f09046a96db5ae Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 May 2020 11:10:50 -0500
Subject: [PATCH] Generalize find fastq after fetch
---
workflow/scripts/bdbagFetch.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
index d009ed8..a5ee262 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -3,9 +3,9 @@
if [ -z "${3}" ]
then
bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
- for i in $(find */ -name "*.R*.fastq.gz")
+ for i in $(find */ -name "*R*.fastq.gz")
do
- path=${2}$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz")
+ path=16-TA16$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz")
cp ${i} ./${path}
done
elif [ "${3}" == "TEST" ]
--
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