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Provide bwa mem / bwa mem2 mode #106

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apeltzer opened this issue Feb 3, 2021 · 2 comments
Open

Provide bwa mem / bwa mem2 mode #106

apeltzer opened this issue Feb 3, 2021 · 2 comments
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enhancement New feature or request
Milestone
2.1

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@apeltzer
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apeltzer commented Feb 3, 2021

Only for required genome fasta / subset for HLA to make mapping much faster and less memory intensive.
@christopher-mohr christopher-mohr added the enhancement New feature or request label Feb 3, 2021
@christopher-mohr christopher-mohr added this to the 1.1.3 milestone Feb 3, 2021
@apeltzer apeltzer modified the milestones: 1.1.3, 2.0 Mar 17, 2021
@christopher-mohr christopher-mohr modified the milestones: 2.0, 2.1 Oct 13, 2022
@chrstphdm
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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
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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.

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@apeltzer @christopher-mohr @chrstphdm