From 56d352504ed5757f9502a3a973ecad405ae3a261 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 19 Jan 2021 19:41:56 -0600
Subject: [PATCH] Allow .R[1,2] and _R[1,2] fastqs
---
CHANGELOG.md | 4 ++--
workflow/scripts/bdbag_fetch.sh | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d35003f..03e3146 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,9 +6,9 @@
* Remove parsing restrictions for submitted stranded/spike/species (#105, #106)
* Pass unidentified ends instead of overwriting it as unknown
* Move fastqc process before trim to catch fastq errors (#107)
-* Only use fastq's that match *.R[1,2].fastq.gz naming convention (#107)
+* Only use fastq's that match *[_.]R[1-2].fastq.gz naming convention (#107)
* Add error output for no fastq's
-* Update input bag export config to only fetch fastq's that match *.R[1,2].fastq.gz naming convention
+* Update input bag export config to only fetch fastq's that match *[_.]R[1-2].fastq.gz naming convention
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
diff --git a/workflow/scripts/bdbag_fetch.sh b/workflow/scripts/bdbag_fetch.sh
index ea2efd0..45ee14a 100644
--- a/workflow/scripts/bdbag_fetch.sh
+++ b/workflow/scripts/bdbag_fetch.sh
@@ -18,7 +18,7 @@ if [ "${validate}" != "is valid" ]
then
exit 1
fi
-for i in $(find */ -name "*.R[1-2].fastq.gz")
+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}
--
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