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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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Allow annotation steps to be be turned on and off in config. #154

Closed LeeBergstrand closed 2 months ago

LeeBergstrand commented 2 months ago

Addresses issue https://github.com/rotary-genomics/rotary/issues/140

Allows the user to select what annotations to run based on a list of annotation types in the config file.

annotations: ['DFAST_Func', 'EggNOG', 'GTDBTk', 'CheckM2', 'coverage']

Changes:

  1. A Python class for creating objects that can be queried to determine what annotation steps should run.
  2. Code that uses this class to determine what annotations to run.
  3. Pass the --no_func_anno flag to DFAST if you don't want the light annotation to occur.
  4. Use {sample}_genome.fna from DFAST as an indicator to symlink the log files to go inside annotation_summary.zip as, at minimum, DFAST is always run, unlike the other annotation types.

@jmtsuji Thoughts?

LeeBergstrand commented 2 months ago

@LeeBergstrand Nice enhancement -- thank you for working on this while I focus on utility development! In my review, I've flagged a couple minor things to consider enhancing or fixing, but otherwise, looks great. I'd be happy to take a second look before it's finally merged. Thanks!

@jmtsuji Great job with the feedback. Good bug catch and feature request. Requesting that you review it again.