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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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Looper should speak pephub #341

Closed nsheff closed 12 months ago

nsheff commented 1 year ago

What if you could looper run pephub://databio/project ?

In other words, instead of passing sample metadata via a file, you pass it via registry path. Looper needs to learn to speak the PEPhub API.

khoroshevskyi commented 1 year ago

Issue #342 blocks this one. Looper config should be decoupled from PEP

nsheff commented 1 year ago

@Khoroshevskyi can you add a section in the docs on how to do this? Actually I think it would be great to:

  1. [ ] include the example config in the docs to show how to set it up.
  2. [ ] add an example to hello_looper to show how to run it?
  3. [ ] update the looper init functionality to be able to also populate it with pifaces
nsheff commented 1 year ago

@khoroshevskyi can you comment on the status of this documentation?