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seqkit: switch to sample2 subcommand#11145

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seqkit: switch to sample2 subcommand#11145
bounlu wants to merge 1 commit intomasterfrom
bounlu-patch-1

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@bounlu bounlu commented Apr 10, 2026

Switched to sample2 for a more accurate and memory efficient option: https://bioinf.shenwei.me/seqkit/usage/#sample2

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Closes #XXX

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Switched to `sample2` for a more accurate and memory efficient option: https://bioinf.shenwei.me/seqkit/usage/#sample2
@jfy133 jfy133 changed the title Update main.nf seqkit: switch to sample2 subcommand Apr 10, 2026
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@bounlu I think this should instead be a separate module - it's an entirely new subcommand, and maybe have slightly different output (based on the description). IOt oculd be people are theoretically reliant on the original implementation, so that should stay as is.

This would be a relatively easy module to do though, you just copy over the existing module just adding 2 to every reference of teh sample subcommand/name

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@mashehu mashehu left a comment

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then this module needs to be called seqkit/sample2, i.e. a new module needs to be created for this

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