Make compatible with pungi updates

rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements

BSD 3-Clause "New" or "Revised" License

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Closed LeeBergstrand closed 4 months ago

LeeBergstrand commented 4 months ago

Changes to rotary to make it compatible with the latest pungi updates detailed here: https://github.com/rotary-genomics/pungi/pull/3

move pathing to the default config back into rotary rather than pungi. Utilizes pungi's get_config_path function.
pass the config object to setup_run_directory rather than the pass.
some minor variable renaming and documentation improvements.

LeeBergstrand commented 4 months ago

miving to dedicated dev branch for lee