qiime2 / q2galaxy

Generate Galaxy tool descriptions automatically from QIIME 2 actions.
BSD 3-Clause "New" or "Revised" License
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Ensure that hidden actions are rendered in q2galaxy #57

Open ebolyen opened 4 weeks ago

ebolyen commented 4 weeks ago

Improvement Description Typically we use hidden actions for the inner part of a parallel pipeline loop, e.g.

def some_parallel_pipeline():
  ...
  collection = partition_data()
  for key, val in collection.items():
    result[key] =  _hidden_method(val)
  viz = collate_data(result)
  ...

where partition_data, _hidden_method, and collate_data are all qiime2 actions.

With Galaxy, it is better to use the built-in for-each on a collection which will play nicely with whatever scheduler is present and will accomplish the same goal as the pipeline. So the user should be using the underlying actions directly instead of the pipeline.

ebolyen commented 4 weeks ago

This is more interesting when our metagenome distro arrives on the scene, as amplicon doesn't tend to use these features