From 523e083f15400e669c862fe36bcdb90df31fe321 Mon Sep 17 00:00:00 2001 From: Till Hartmann Date: Wed, 13 Nov 2024 13:54:40 +0100 Subject: [PATCH] fix: unconditionally add optitype and arcashla sub_steps --- snappy_pipeline/workflows/hla_typing/__init__.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/snappy_pipeline/workflows/hla_typing/__init__.py b/snappy_pipeline/workflows/hla_typing/__init__.py index c39060f12..a2b8d2b04 100644 --- a/snappy_pipeline/workflows/hla_typing/__init__.py +++ b/snappy_pipeline/workflows/hla_typing/__init__.py @@ -300,14 +300,7 @@ def default_config_yaml(cls): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs, config_model_class=HlaTypingConfigModel) - sub_steps = [LinkInStep, LinkOutStepPart] - for tool in self.config.tools: - if self.config.get(str(tool)): - match tool: - case "optitype": - sub_steps.append(OptiTypeStepPart) - case "arcashla": - sub_steps.append(ArcasHlaStepPart) + sub_steps = [LinkInStep, LinkOutStepPart, OptiTypeStepPart, ArcasHlaStepPart] self.register_sub_step_classes(tuple(sub_steps)) #: Mapping from library name to library object self.ngs_library_name_to_ngs_library = OrderedDict()