Add module for TaxonKit name2taxid

[mahesh-panchal]

PR checklist

Adds the module TaxonKit name2taxid

Closes #XXX

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[mahesh-panchal]

@nf-core-bot fix linting

[nvnieuwk]

I see why you would want the input like this, but I'm not sure if it follows the guidelines since the actual input is a file.

[nvnieuwk]

The file could be easily made using the .collectFile() operator

[mahesh-panchal]

I was just following the docs https://bioinf.shenwei.me/taxonkit/usage/#name2taxid.

Although how do you mean with collectFile(). The output of that is file and not [ meta, file ].

[nvnieuwk]

Yes true, but that's nothing some channel logic can't handle :).

@maintainers what are your opinions on this?

[mahesh-panchal]

It's not particularly easy for a new developer though:

    Channel.of( [ id: 'test', taxid: 1234 ] )
        .tap { ch_data }
        .collectFile( newLine: true ) { meta -> [ "${meta.id}.tsv", "$meta.taxid" ] }
        .map{ file -> [ file.baseName , file ] }
        .join( ch_data.map { meta -> [ meta.id, meta ] }, by: 0 )
        .map{ id, idfile, meta -> [ meta, idfile ] }

[mahesh-panchal]

The value is mandatory if there's no file ( and I don't plan on generating that file )

[jfy133]

What is the difference between name and names_txt? As in you can supply a string versus a file?

[mahesh-panchal]

Yes, you can pipe in the name, or provide a list of names.

[jfy133]

Could have two separate optional input channels, one for string only and one for file (but are mutually exclusive)?

Might look alittle ugly, would be relatively easy for for a pipeline dev to put an [] in the channel they don't want with a (multi)Map?

[mahesh-panchal]

I think that's just adding unnecessary complexity to have to use multiMap to make this input.
Either way the input will likely need to be formed using a map

[jfy133]

Minor things, but otherwise no blockers from my end now given the input channel structure guidelines appear to be a bit in flux

[jfy133]

Maybe specify it should be the directory that get's supplied (presumably? from my knowledge of taxdump.tar.gz)

[mahesh-panchal]

In my case it's specifically that file that I use outside of this module.

[jfy133]

I have a mini set of (working) taxdump files for createtaxdb:

https://github.com/nf-core/test-datasets/tree/createtaxdb/data/taxonomy

You're welcome to tar.gz them and add to test datasets if you want to speed up tests if slow?

[mahesh-panchal]

The tests don't seem slow, but let me see if there's a difference.