Function phenopacket_pipeline should probably be a class

[SmartMonkey-git]

Probably, Daniel will also point this out and I will hold back with my recommendations, as what should be a class and what not, but I think, we all agree that this function should be a class.

class RarelinkPipeline:

    def __init__(self,
                 mapping_configs: Optional[Dict[str, Any]] = None,
                 timeout: int = 3600,
                 progress_callback: Optional[Callable] = None,
                 validation_callback: Optional[Callable] = None,
                 ):
        self._mapping_configs = mapping_configs or {}
        self._timeout = timeout
        self._progress_callback = progress_callback
        self._validation_callback = validation_callback

    def run(self,
            input_data: list,
            output_dir: str,
            created_by: str,
            ) -> PipelineResult:
        pass

Something, like this would work. I left out the debug input as either the CLI or the user should set that.