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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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Run related actions not in Runner __call__ #95

Closed stolarczyk closed 5 years ago

stolarczyk commented 5 years ago

raised in discussion with @nsheff a few days ago

Would it be possible to include the following lines in the Runner.__call__?

https://github.com/pepkit/looper/blob/0d2db9d57acf087e8ae9cf066d0e7d7f6dbf050b/looper/looper.py#L846-L864

This steps are executed only in case the run command is called anyway.

We need to use Runner() in caravel. Using current implementation would mean that and this steps would need to be reproduced and maintained in two places.

vreuter commented 5 years ago

OK, if you now pull argparser_caravel you should get the updates.