From ac401bbb6939f1211db4cfe57f15d632e4e7a152 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 14:16:30 +0200
Subject: [PATCH] create temporary directory and clean up on exit

---
 src/agat/agat_sq_stat_basic/test.sh | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/agat/agat_sq_stat_basic/test.sh b/src/agat/agat_sq_stat_basic/test.sh
index 92f13775..12bd28cd 100644
--- a/src/agat/agat_sq_stat_basic/test.sh
+++ b/src/agat/agat_sq_stat_basic/test.sh
@@ -6,21 +6,28 @@ set -eo pipefail
 ## VIASH END
 
 test_dir="${meta_resources_dir}/test_data"
-out_dir="${meta_resources_dir}/out_data"
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
+
 
 echo "> Run $meta_name with test data"
 "$meta_executable" \
   --gff "$test_dir/1.gff" \
-  --output "$out_dir/output.txt" 
+  --output "$TMPDIR/output.txt" 
   
 echo ">> Checking output"
-[ ! -f "$out_dir/output.txt" ] && echo "Output file output.txt does not exist" && exit 1
+[ ! -f "$TMPDIR/output.txt" ] && echo "Output file output.txt does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "$out_dir/output.txt" ] && echo "Output file output.txt is empty" && exit 1
+[ ! -s "$TMPDIR/output.txt" ] && echo "Output file output.txt is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$out_dir/output.txt" "$test_dir/agat_sq_stat_basic_1.gff"
+diff "$TMPDIR/output.txt" "$test_dir/agat_sq_stat_basic_1.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.txt does not match expected output"
   exit 1