From 620ef9e445d889ba06336992ac6184117458e1f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=98ens-ftricomi=E2=80=99?= Date: Fri, 6 Oct 2023 11:04:11 +0100 Subject: [PATCH] fixed function's input pramaters --- .../tools/anno/transcriptomic_annotation/scallop.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/python/ensembl/tools/anno/transcriptomic_annotation/scallop.py b/src/python/ensembl/tools/anno/transcriptomic_annotation/scallop.py index 8bace4f..0fc9be9 100644 --- a/src/python/ensembl/tools/anno/transcriptomic_annotation/scallop.py +++ b/src/python/ensembl/tools/anno/transcriptomic_annotation/scallop.py @@ -178,6 +178,11 @@ class InputSchema(argschema.ArgSchema): default="scallop", description="Scallop software path", ) + stringtie_bin = argschema.fields.String( + required=False, + default="stringtie", + description="Scallop software path", + ) prlimit_bin = argschema.fields.String( required=False, default="prlimit", @@ -199,5 +204,5 @@ def main() -> None: disable_existing_loggers=False, ) run_scallop( - mod.args["output_dir"], mod.args["scallop_bin"], mod.args["prlimit_bin"], mod.args["memory_limit"] + mod.args["output_dir"], mod.args["scallop_bin"], mod.args["prlimit_bin"], mod.args["stringtie_bin"], mod.args["memory_limit"] )