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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 skip scorpio parameter to pangolin #234

Closed MarieLataretu closed 2 years ago

MarieLataretu commented 2 years ago

From pangolin version 4 on the linage assignment is done by Usher. However scorpio overwrites the results which leads to a lot unassigned samples.

I'll add a parameter to skip scorpio in the pangolin run

MarieLataretu commented 2 years ago

for now the default is that scorpio is not skipped and can be skipped with pangolin_skip_scorpio