Ensure unique contig names across assemblies, for chaining pipeline with magmap

[amizeranschi]

Description of feature

Hello,

I've created assemblies with nf-core/mag using MEGAHIT and now I'm trying to align the reads to the assemblies using nf-core/magmap. The problem is that the latter concatenates the assemblies before creating an index for mapping with BBTools. This results in lots of duplicate contig names in the reference index, because MEGAHIT uses the same contig naming scheme for each assembly that it creates, and there doesn't seem to be a way to change this behavior in order to ensure unique contig names across all of the assemblies.

It would be great to have a setting for ensuring that the pipeline generates unique contig names.

Relevant thread on Slack: https://nfcore.slack.com/archives/C070369GP7T/p1735754871023769