From b8499b531924c46f67bd09454df55f58bf7ff465 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 10:50:50 +0200
Subject: [PATCH] # create temporary directory and clean up on exit

---
 src/agat/agat_sp_add_introns/test.sh | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/agat/agat_sp_add_introns/test.sh b/src/agat/agat_sp_add_introns/test.sh
index 429b3b5c..35149df8 100644
--- a/src/agat/agat_sp_add_introns/test.sh
+++ b/src/agat/agat_sp_add_introns/test.sh
@@ -3,23 +3,28 @@
 ## VIASH START
 ## 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=$(mktemp --tmpdir "$meta_temp_dir")
+function clean_up {
+ 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.gff" 
+  --output "$TMPDIR/output.gff" 
 
 echo ">> Checking output"
-[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$out_dir/output.gff" "$test_dir/agat_sp_add_introns_1.gff"
+diff "$TMPDIR/output.gff" "$test_dir/agat_sp_add_introns_1.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"
   exit 1