Provide bwa mem / bwa mem2 mode

nf-core / hlatyping

Precision HLA typing from next-generation sequencing data

https://nf-co.re/hlatyping

MIT License

63 stars 30 forks source link

Provide bwa mem / bwa mem2 mode #106

Open apeltzer opened 3 years ago

apeltzer commented 3 years ago

Only for required genome fasta / subset for HLA to make mapping much faster and less memory intensive.

chrstphdm commented 2 years ago

Hi there.

Very good idea ! What about using the new genome mapperDRAGMAP. The nf-core module is available (but I never used it to be honest).

apeltzer commented 2 years ago

Since the pipeline is now rewritten in DSL2, we could have a subworkflow that handles the choice of mapper(s) directly, users can then choose what to use.