From 66591ecd4ec0f56b7a315b643c22da19869a655e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 14 Feb 2020 13:29:16 -0600
Subject: [PATCH] Fix if not exist in bdbagFetch.sh
---
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 8a6c780..fc0ffab 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -1,6 +1,6 @@
#!/bin/bash
-if [ -z ${3} ]
+if [ -z "${3}" ]
then
bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
for i in $(find */ -name "*.R*.fastq.gz")
@@ -8,7 +8,7 @@ bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
path=${2}$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz")
mv ${i} ./${path}
done
-elif [ ${3} == "TEST" ]
+elif [ "${3}" == "TEST" ]
then
bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
fi
\ No newline at end of file
--
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