From d9d4d35a3ef7142b255269c99f1c08259380bbe7 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 Jan 2021 22:49:29 -0600
Subject: [PATCH] Move new bdbag fetch code from test
---
workflow/scripts/bdbag_fetch.sh | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/workflow/scripts/bdbag_fetch.sh b/workflow/scripts/bdbag_fetch.sh
index 117340b..761b9c3 100644
--- a/workflow/scripts/bdbag_fetch.sh
+++ b/workflow/scripts/bdbag_fetch.sh
@@ -2,15 +2,7 @@
if [ -z "${3}" ]
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")
- cp ${i} ./${path}
- done
-elif [ "${3}" == "TEST" ]
-then
- bdbag --materialize ${1} --debug
+ bdbag --materialize ${1} --debug
validateError=true
bdbag --validate full ${1} && validateError=false
if validateError
@@ -27,4 +19,12 @@ then
then
exit 1
fi
+ for i in $(find */ -name "*R*.fastq.gz")
+ do
+ path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
+ cp ${i} ./${path}
+ done
+elif [ "${3}" == "TEST" ]
+then
+ bdbag --validate structure --validate-profile ${1} --debug
fi
--
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