nf-core / pangenome

Renders a collection of sequences into a pangenome graph.

https://nf-co.re/pangenome

MIT License

63 stars 16 forks source link

add pgge #38

Closed subwaystation closed 1 year ago

subwaystation commented 3 years ago

nf-core/pangenome feature request

Hi there!

Describe the solution you'd like

Integrate the pangenome graph evaluator pgge.

subwaystation commented 3 years ago

As a short term solution, all functionality of pgge are put into a submodule using the soon-to-be-there docker image based on https://github.com/jmonlong/docker-pgge.

On the long term, all tools in the pgge submodule should become their own module.

This issue depends on https://github.com/pangenome/pgge/issues/16.

subwaystation commented 1 year ago

We will rather use a MUMMER evaluation of the graph, for details see https://www.biorxiv.org/content/10.1101/2023.04.05.535718v1.