Nice addition! Minor suggestions. Wondering if this is actually not a subcommand of a larger tool bio2zarr, which would make the name of the tool modules/nf-core/bio2zarr/vcfpartition, thoughts?

Good question. I think one argument is that bio2zarr is the repository/package name, and vcfpartition exists at the tool level. The package also contains vcf2zarr, which has its own subtools convert, explode etc.

I previously added the modules vcf2zarr/convert and vcf2zarr/explode.

I didn't consider the other tools then, but now I want to work on plink2zarr, so I'm happy to re-think this approach.

Or, more simply, there is no bio2zarr command.

Nice addition! Minor suggestions. Wondering if this is actually not a subcommand of a larger tool bio2zarr, which would make the name of the tool modules/nf-core/bio2zarr/vcfpartition, thoughts?

Good question. I think one argument is that bio2zarr is the repository/package name, and vcfpartition exists at the tool level. The package also contains vcf2zarr, which has its own subtools convert, explode etc.

Are there other commands within the bio2zarr package/repository? If so all would go under bio2zarr/<command name> in my opinion.

But even then, if vcfpartition is the sole tool within the repository name, it's a very generic name 😅 so prefixing with bio2zarr would be nicer.

I previously added the modules vcf2zarr/convert and vcf2zarr/explode.

I didn't consider the other tools then, but now I want to work on plink2zarr, so I'm happy to re-think this approach.

I see why you would opt for that here though... it's a bit nasty from the developers...

When did you add the previous modules? Do you think they are already being used in pipelines, or are they fresh modules that we could rename them (e.g. to `bio2zarr/vcf2zarrexplode)?

Another annoying example i've encoutnered is the conda recipe being called ncbi-datasets but the actual executed command is just datasets (very generic)

But let's also see what other maintainers think... ultimately it's about findabilty at this poitn

One yesterday, one last year. Neither used in pipelines as far as I can tell.

bio2zarr contains:

• vcf2zarr
• plink2zarr
• tskit2zarr
• vcfpartition

I will update the other modules in a follow-up PR. Thank you!