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asalt / bcm-gsea

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validate config file spec #3

Open asalt opened 2 months ago

asalt commented 2 months ago

make a validation routine for basic checks for the config

take as much logic out of main or run scripts as possible

best if we can access params very simply as param$param %||% DEFAULT where param$param requires no modifification and DEFAULT is reasonable deafult.

could fill in params with defaults in param validation routine ahead of time as well, leaving the %||% checks as defensive code

asalt commented 2 months ago

added clean_args func to cli.R to check and set some defaults. shouldn't need to set everything as most NULLs should be handled appropriately downstream. if this isn't the case we could add more parameter handling here as well. there's no actual loading of downstream files from the config here, though, so there's not going to be extensive parameter checking - that mostly happens as-is with default fallbacks, and can simply be re-ran with a correction if something is set incorrectly.

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