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monarch-initiative / pheval.exomiser

Exomiser plugin for PhEval.
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59 allow for multiple output formats from exomiser #60

Closed yaseminbridges closed 2 months ago

yaseminbridges commented 3 months ago

Implemented the specification of specific raw result output formats for Exomiser. This way we will be able to limit the result output to just the JSON if the HTML etc are not required but also provides the opportunity to request other raw output formats if needed.

This will be a breaking change as the config.yaml in the input_dir will need to be updated with this additional field - README.md and skeleton config.yaml have been updated accordingly.

yaseminbridges commented 2 months ago

Seems OK, apart from the list[Path] being used in a couple of places. Why is it that you don't just take the existing application.properties file again?

Fixed now! You said to create the application.properties on the fly a while ago to reduce user error - this way we know exactly where the application.properties is and can configure the properties with what is in the config.yaml.