bokulich-lab / q2-moshpit

MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking
BSD 3-Clause "New" or "Revised" License
3 stars 12 forks source link

MAINT: move partitioning and collating actions to q2-types #172

Open misialq opened 4 months ago

misialq commented 4 months ago

Is your feature request related to a problem? Please describe. Some plugins (e.g. q2-amr) use partitioning and/or collating actions contained in q2-moshpit to facilitate parallelization of their respective actions. This introduces a dependency on q2-moshpit and can sometimes lead to dependency issues. We should move those actions to q2-types as every plugin needs it anyway and it would simplify dependency resolution. Those actions are also directly linked to some types/formats so q2-types seems like a good place for those actions to live.

Describe the solution you'd like Move all the code for partitioning/collating actions to q2-types. This will require adjusting all the actions (here and everywhere else) which use the actions being moved.