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Public-Health-Bioinformatics / cpo-pipeline

An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
MIT License
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Merge Pipeline Phases Into One Unified Pipeline #8

Closed dfornika closed 5 years ago

dfornika commented 5 years ago

We currently have three 'phases' for the pipeline:

  1. assembly
  2. typing
  3. tree

These can be combined into a single pipeline, which will simplify the end-user's task of running the pipeline.

bfjia commented 5 years ago

currently, the assembly and typing portion only supports single isolates. Whereas the 'tree' module requires the use of multiple isolates

dfornika commented 5 years ago

Good point. It's likely that the assembly & typing phases will be run routinely as soon as new samples arrive. Then the tree phase would be run more sporadically. It might make sense to keep those parts separate in some way.