From 0c3d1a1ee5a3fb3a72752ee566a1585ce32d5c69 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 May 2020 17:38:59 -0500
Subject: [PATCH] Fix cp error for fastq names with multiple R1/2
---
workflow/scripts/bdbagFetch.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
index 0bf20f0..606b883 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -5,7 +5,7 @@ then
bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
for i in $(find */ -name "*R*.fastq.gz")
do
- path=${2}.$(echo ${i##*/} | grep -o "R[1,2]").fastq.gz
+ path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
cp ${i} ./${path}
done
elif [ "${3}" == "TEST" ]
--
GitLab