Change how looper determines pipestat configuration

pepkit / looper

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http://looper.databio.org

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Change how looper determines pipestat configuration #411

Closed donaldcampbelljr closed 6 months ago

donaldcampbelljr commented 10 months ago

          - [ ] Per discussion, change how looper determines pipestat configuration, i.e. instead of relying on pipestat's config file, the looper config file should supply the proper information to use pipestat. #

Originally posted by @donaldcampbelljr in https://github.com/pepkit/looper/issues/409#issuecomment-1689987634

donaldcampbelljr commented 10 months ago

This should be addressed with PR: https://github.com/pepkit/looper/pull/409

donaldcampbelljr commented 10 months ago

Still some polish that needs to be achieved.

[x] ensure db or file backend configs are not duplicated for sample or project in the config file.
[x] ensure .looper.yaml configuration works as expected.
[x] ensure db backend can be used with this new approach of setting pipestat configurations parameters via looper config as it now uses config_dict as an input to pipestat instead of config_file (i.e. check pipestat logic).