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PMCC-BioinformaticsCore / janis-bioinformatics

Repository of bioinformatics tools for the pipelines module
GNU General Public License v3.0
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Refactor GATK4 tool IDS #90

Open illusional opened 3 years ago

illusional commented 3 years ago

Currently, it's up to each GATK4 tool to declare it's own tool(self): -> str, it would be much better (way more consistent), if the Gatk4 tool base declared the ID as:

class Gatk4ToolBase(BioinformaticsTool, ABC):
    def tool(self) -> str:
        return "Gatk4" + self.gatk_command()
    # other tool definitions

Removing the other GATK def tool lines from the GATK tools is the time-consuming bit.