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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
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Add option for BBTools Clumpify optical deduplication #547

Open funnell opened 1 month ago

funnell commented 1 month ago

Description of feature

Hello,

It would be nice to have the option of using BBTools Clumpify for deduplication as it has the option of performing optical deduplication, instead of PCR deduplication. Clumpify dedup also has recommended parameters for different sequencing platforms, so it would be good to be able to specify these parameters. And/or perhaps allow providing the sequencing platform for each sample/run and have the pipeline automatically set those parameters.

jfy133 commented 1 month ago

There is even an existing nf-core module for it! https://nf-co.re/modules/bbmap_clumpify/

I don't see why not! 👍