Hi everyone, I am running nf-core/mag (v5.2.0) with long-read assemblies (Flye) and exploring ways to improve assembly accuracy using short-read polishing (e.g. Pilon/NextPolish). From what I understand, polishing is not currently part of the nf-core/mag workflow, so I wanted to ask: Is there any recommended way to integrate short-read polishing within nf-core/mag? Or is the preferred approach to perform polishing externally and then provide the polished assemblies via

--assembly_input

? Also, are there any plans to support hybrid polishing workflows in future versions of the pipeline? Thanks in advance!

Not currently supported, and there is not an immediate way to activate it with external tools except for that you suggest about

--asssembly_input

But there is a discussion exactly about polishing a few days ago! https://nfcore.slack.com/archives/CE9MS66BS/p1773852968755209 Please feel free to leave any thoughts/comments