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Add option for BBTools Clumpify optical deduplication #547

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funnell opened this issue Oct 22, 2024 · 1 comment
Open

Add option for BBTools Clumpify optical deduplication #547

funnell opened this issue Oct 22, 2024 · 1 comment
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enhancement Improvement for existing functionality

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@funnell
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funnell commented Oct 22, 2024

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.

@funnell funnell added the enhancement Improvement for existing functionality label Oct 22, 2024
@jfy133
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jfy133 commented Oct 22, 2024

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

I don't see why not! 👍

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