From 07c81f920b77ace22c3f7c9a2c37f46fafe836b1 Mon Sep 17 00:00:00 2001
From: Zachery Dickson <zadick@virome.it.helsinki.fi>
Date: Wed, 5 Jun 2024 11:43:00 +0300
Subject: [PATCH] Allowed input_data to be symbolic links - added -L to file
 command when checking for gzipped input

---
 src/TRACESPipe.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/TRACESPipe.sh b/src/TRACESPipe.sh
index 8ed9032..6ae2bfc 100755
--- a/src/TRACESPipe.sh
+++ b/src/TRACESPipe.sh
@@ -166,8 +166,8 @@ CHECK_META_INFO () {
 #
 #
 CHECK_GZIP_FILES () {
-  FILE_GZ1=`file ../input_data/$1 | grep gzip | wc -l`;
-  FILE_GZ2=`file ../input_data/$2 | grep gzip | wc -l`;
+  FILE_GZ1=`file -L ../input_data/$1 | grep gzip | wc -l`;
+  FILE_GZ2=`file -L ../input_data/$2 | grep gzip | wc -l`;
   if [[ "$FILE_GZ1" != "1" ]] || [[ "$FILE_GZ2" != "1" ]];
     then
     echo -e "\e[31mERROR: the input reads are not gzipped!\e[0m"