From 0c0407f928123f5cd636f51326d4248a5f851706 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 May 2020 17:22:10 -0500
Subject: [PATCH] Change fetched fastq's mv to cv... mv was truncating some
files
---
workflow/scripts/bdbagFetch.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
index fc0ffab..d009ed8 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -2,13 +2,13 @@
if [ -z "${3}" ]
then
-bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
+ 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.\.fastq\.gz")
- mv ${i} ./${path}
+ cp ${i} ./${path}
done
elif [ "${3}" == "TEST" ]
then
bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
-fi
\ No newline at end of file
+fi
--
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