nf-core/hlatyping

Add yara indexing to the pipeline

Closed this issue · 3 comments

szymonwieloch commented

Hi!

This issue is related to this one: #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

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

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christopher-mohr commented

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?

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apeltzer commented

Yes please