Add option --fix to update the meta.yml file of subworkflows.
#3077
Conversation
…ows-meta-yml-restructure
… running prettier to meta.yml file
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Needs nf-core/modules#6679 to be merged at the same time. |
| if self.component_type == "modules": | ||
| inputs_table.add_column("Pattern", justify="right", style="green") | ||
| elif self.component_type == "subworkflows": | ||
| inputs_table.add_column("Structure", justify="right", style="green") |
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because this in the following is basically the same, like the inputs table, can't we just have a generic generate_params_table function to reduce code duplication?
| @@ -170,65 +171,95 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st | |||
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| def get_inputs_from_main_nf(self) -> None: | |||
| """Collect all inputs from the main.nf file.""" | |||
| inputs: list[list[dict[str, dict[str, str]]]] = [] | |||
| inputs: Any = [] # Can be 'list[list[dict[str, dict[str, str]]]]' or 'list[str]' | |||
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| inputs: Any = [] # Can be 'list[list[dict[str, dict[str, str]]]]' or 'list[str]' | |
| inputs: Union[List[List[Dict[str, Dict[str, str]]]],List[str]] = [] |
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This wasn't working, because we append one of the types later on :( I learnt about the overload decorator, but in our case it's not a function.
| @@ -230,3 +237,56 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False): | |||
| self.failed += warned | |||
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| self.failed += [LintResult(swf, *s) for s in swf.failed] | |||
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| def update_meta_yml_file(self, swf): | |||
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can't this be shared component code between modules and subworkflows?
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It is not the same structure, subworkflows have the channel name and description and then we will add a new level called structure which describes the channel components
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but that can be handled like pattern on a modules level, no?
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but we want the description of the input and output channels for the subworkflow, at the meta.yml level we don't know about the modules.
Follow up from #3028 and #3032
Add the option
--fixto update themeta.ymlfile of subworkflows.