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jts / ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
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Add pangolin analysis mode option #103

Closed DarianHole closed 2 years ago

DarianHole commented 2 years ago

Was looking to change the pangolin analysis type while running ncov-tools and I didn't see any configuration options for it so I've attempted to add it in with my limited snakemake knowledge.

Pangolin 4 lets the user specify an analysis mode from "fast" or "accurate" with the --analysis-mode argument. This change is adding that in with the default set to "accurate" as is the same with the tool itself.

I am not sure how this affects the pangolin_version: "3" option so it might need a few changes to accommodate the backwards compatibility aspect there

Cheers

rdeborja commented 2 years ago

additional changes made, merged this PR with #104