add set -eo pipefail to test

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}"}

src/agat/agat_sp_add_introns/test.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e
+set -eo pipefail
 
 ## VIASH START
 ## VIASH END