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nf-core / modules

Repository to host tool-specific module files for the Nextflow DSL2 community!
https://nf-co.re/modules
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gffread nucleotide to protein #4152

Open chriswyatt1 opened 8 months ago

chriswyatt1 commented 8 months ago

Is your feature request related to a problem? Please describe

gffread has many different functions, the one used in this module converts a gff file to gtf . However gffread also converts an input gff file and a genome (fasta) into a protein.fasta file. This functionality is lacking. I am happy to write up this module to add this, but am not sure which direction to follow

Describe the solution you'd like

I assume this needs to be a new module (as the inputs/output types will be quite different). If we make this a new module, it will mean the gffread module for gff to gtf will need to have a subfolder name... Will this mess up everyones pipelines if I create a new subfolder?

gffread -y -g

Describe alternatives you've considered

Are there other modules in nf-core that simply converts genome/annotation to protein fastas? or should I just combine gffread into the next module I want to make (orthofinder) so that I don't need to make a new gffread module (a bit of a messy option, I think, but would work).

Additional context

No response

GallVp commented 3 weeks ago

Hi @chriswyatt1

I had the same thoughts and changed the current gffread module to close this gap. Can you kindly check that the current version satisfies your needs?

https://github.com/nf-core/modules/blob/master/modules/nf-core/gffread/main.nf

chriswyatt1 commented 3 weeks ago

Thanks, looks great.

I should be able to check later today.

chriswyatt1 commented 3 weeks ago

Yes @GallVp, all looks great. I can use it for my use case too now, thanks!