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fix: unconditionally add optitype and arcashla sub_steps #547

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Nov 13, 2024
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fix: unconditionally add optitype and arcashla sub_steps #547

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9 changes: 1 addition & 8 deletions snappy_pipeline/workflows/hla_typing/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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()
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