Add CPU support for Guppy basecalling

replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data

https://case-group.github.io/

GNU General Public License v3.0

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Add CPU support for Guppy basecalling #20

Closed hoelzer closed 3 years ago

hoelzer commented 3 years ago

Compare: https://gitlab.com/RKIBioinformaticsPipelines/nanoqc/-/blob/master/modules/guppy.nf

We could provide for users w/o GPU access a CPU Guppy version. At the moment, I think, only GPU is supported.

replikation commented 3 years ago

cpu support is ultra slow or? we are talking weeks or?

hoelzer commented 3 years ago

cpu support is ultra slow or? we are talking weeks or?

Yeah, super slow and only feasible on a large machine with 48 cores or so. But from what I know, people lacking a GPU are doing this right now :) Maybe I can easily move the code pieces linked above into poreCov and add --cpu flag.

replikation commented 3 years ago

yep ill add. just takes more time to validate if its running properly