From 7a22888bc42b2136a37077d4fada5a07d51db5b2 Mon Sep 17 00:00:00 2001 From: Leila011 Date: Mon, 19 Aug 2024 11:03:35 +0200 Subject: [PATCH] create temporary directory and clean up on exit --- .../test.sh | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/src/agat/agat_sp_filter_feature_from_kill_list/test.sh b/src/agat/agat_sp_filter_feature_from_kill_list/test.sh index 0e79c803..a86deb30 100644 --- a/src/agat/agat_sp_filter_feature_from_kill_list/test.sh +++ b/src/agat/agat_sp_filter_feature_from_kill_list/test.sh @@ -4,22 +4,28 @@ ## 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 "$test_dir/1.gff" \ --kill_list "$test_dir/kill_list.txt" \ - --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_filter_feature_from_kill_list_1.gff" +diff "$TMPDIR/output.gff" "$test_dir/agat_sp_filter_feature_from_kill_list_1.gff" if [ $? -ne 0 ]; then echo "Output file output.gff does not match expected output" exit 1