From 821a0f05ca8eb6eb427250a19ed8193b099744c8 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 12 Feb 2021 23:16:00 -0600
Subject: [PATCH] Move fastq count before cp
---
rna-seq.nf | 11 ++---------
workflow/scripts/bdbag_fetch.sh | 2 ++
2 files changed, 4 insertions(+), 9 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 5b15367..693199e 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -257,12 +257,6 @@ process getData {
hostname > ${repRID}.getData.log
ulimit -a >> ${repRID}.getData.log
- # link deriva cookie for authentication
- #echo -e "LOG: linking deriva cookie" >> ${repRID}.getData.log
- #mkdir -p ~/.bdbag
- #cp `readlink -e cookies.txt` ~/.bdbag/deriva-cookies.txt
- #echo -e "LOG: linked" >> ${repRID}.getData.log
-
# get bag basename
replicate=\$(basename "${inputBag}")
echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log
@@ -274,10 +268,9 @@ process getData {
# bag fetch fastq's only and rename by repRID
echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log
- sh ${script_bdbagFetch} \${replicate::-13} ${repRID}
+ fastqCount=\$(sh ${script_bdbagFetch} \${replicate::-13} ${repRID})
echo -e "LOG: fetched" >> ${repRID}.getData.log
-
- fastqCount=\$(find . -name '*.fastq.gz' | wc -l)
+
if [ "\${fastqCount}" == "0" ]
then
touch dummy.R1.fastq.gz
diff --git a/workflow/scripts/bdbag_fetch.sh b/workflow/scripts/bdbag_fetch.sh
index 59e1136..d336829 100644
--- a/workflow/scripts/bdbag_fetch.sh
+++ b/workflow/scripts/bdbag_fetch.sh
@@ -18,8 +18,10 @@ if [ "${validate}" != "is valid" ]
then
exit 1
fi
+count=$(find */ -name "*[_.]R[1-2].fastq.gz" | wc -l)
for i in $(find */ -name "*[_.]R[1-2].fastq.gz")
do
path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
cp ${i} ./${path}
done
+echo ${count}
--
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