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nf-core / hlatyping

Precision HLA typing from next-generation sequencing data
https://nf-co.re/hlatyping
MIT License
63 stars 30 forks source link

Add yara indexing to the pipeline #112

Closed szymonwieloch closed 2 years ago

szymonwieloch commented 3 years ago

Hi!

This issue is related to this one: https://github.com/nf-core/hlatyping/issues/111

I would like to be able to run the pipeline using just a fasta file as a reference. Internally the pipeline should run the yara_indexer in the right way and produce all the indexes that are later used by OptiType. you would use it in the following way:

nextflow run nf-core/hlatyping --reference ref.fasta.gz

I believe that this solution would not only be the easiest for users, but I would also be the best documentation of the procedure used to generate index files.

apeltzer commented 3 years ago

We added a YARA index module for DSL2, which means there is going to be a YARA index possibility for the new planned release.

christopher-mohr commented 2 years ago

YARA indexing has been added to the pipeline with the DSL2 port. I would suggest to close this issue and make a new one for the possibility to provide a FASTA file as reference. This can then be implemented for 2.1. What do you think @apeltzer?

apeltzer commented 2 years ago

Yes please