nf-core/deepmodeloptim
[future][discussion] how to incorporate external modules ?
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#195 geöffnet am 23.10.2024
enhancementhelp wanted
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Beschreibung
Description of feature
Allow for data processing to be done by modules external from the stimulus-py package and not necessarily in python
Example :
Splitting a sequence dataset could be done using pairwise similarity + kmeans There are many tools doing pairwise similarity, some even gpu accelerated, and some nf-core modules could do this
Current way to do this would be to wrap the method in python and bumb the pip package but it isn't the nf-core way, it would be much better if instead, we could re-use modules with some minor overhead for format/data processing.
This should be done while considering :
- whether the tool should be ran or not depends on the experiment config
- code should be kept clean (there are many tools that could interface with data processing - and the number will keep growing ), chaining IF/ELSE is not an option
- good error handling (i.e. blast can't run on images for instance)