(Pipeline Implementation) Points to clarify with devbio

[islean]

We have in our codebase certain parts of the code which are unclear to us system developers. The intent should be documented and the code rewritten in some instances. This issue will be used to gather points to discuss with the devbio people.

[islean]

There is awhile True loop in the analysis api:

def replace_values_in_params_file(self, workflow_parameters: dict) -> dict:
        replaced_workflow_parameters = copy.deepcopy(workflow_parameters)
        """Iterate through the dictionary until all placeholders are replaced with the corresponding value from the dictionary"""
        while True:

[islean]

Could we name the variables in servers a bit more explicitly? Params -> parameters_file and type hint it as path in cg for example?

[islean]

The get_sex_code method returns ints as a string but the intent seem to be to use them as ints. We should consider clearing this up.

[islean]

_extract_read_files should only have a single boolean input, not two.

[islean]

Maybe move def _get_data_analysis_type(self, case_id: str) -> str: to the store