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nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples
https://nf-co.re/viralrecon
MIT License
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Allow skipping `freyja boot` #417

Closed tavareshugo closed 1 month ago

tavareshugo commented 4 months ago

Description of feature

To save some computation, it may sometimes be desirable to skip freyja's bootstrapping step.

My suggestion would be to allow using --freyja_repeats 0. At the moment, using it like this throws an internal error from freyja. But maybe viralrecon could interpret 0 (or any negative number, for that matter) as meaning "don't run the bootstrap step".

In fact, it may be worth considering --freyja_repeats 0 as the default, in case those processing clinical isolates forget to do --skip_freyja and end up spending a lot of unnecessary compute time bootstrapping.

I guess an alternative would be to add a new option --skip_freyja_boot.

Joon-Klaps commented 2 months ago

Good point. I'll add a skip_freyja_boot and make sure that repeats are >0