From 8c32ea3eb0f3bbff029fd4b776504643b7abfeb3 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 13:32:30 +0200
Subject: [PATCH] add set -eo pipefail to test

---
 src/agat/agat_convert_genscan2gff/script.sh | 21 +++++++++++++++++++++
 src/agat/agat_sp_add_introns/test.sh        |  2 +-
 2 files changed, 22 insertions(+), 1 deletion(-)
 create mode 100644 src/agat/agat_convert_genscan2gff/script.sh

diff --git a/src/agat/agat_convert_genscan2gff/script.sh b/src/agat/agat_convert_genscan2gff/script.sh
new file mode 100644
index 00000000..38afb084
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/script.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# run agat_convert_genscan2gff
+agat_convert_genscan2gff.pl \
+  --genscan "$par_genscan" \
+  --output "$par_output" \
+  ${par_source:+--source "${par_source}"} \
+  ${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
+  ${par_inflate_off:+--inflate_off} \
+  ${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
+  ${par_verbose:+--verbose} \
+  ${par_config:+--config "${par_config}"}
\ No newline at end of file
diff --git a/src/agat/agat_sp_add_introns/test.sh b/src/agat/agat_sp_add_introns/test.sh
index 54ec04dc..5533e438 100644
--- a/src/agat/agat_sp_add_introns/test.sh
+++ b/src/agat/agat_sp_add_introns/test.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e
+set -eo pipefail
 
 ## VIASH START
 ## VIASH END