Hello, I am currently using the metatdenovo pipeline and I'm focusing on the functional module. I have previously worked with the nf-core/mag pipeline and I would like to know if it is possible to give as input multiple assemblies to run the pipeline. So far I have tested with only one assembly as input and it has worked. I've tested with more assemblies but an error message occurs. I don't know if it is due to the format or because the option of multiple assemblies is not present in the workflow. Can somebody help me please?

No, that's not possible and is actually a bit away from the intentions of the pipeline. With a typical metatranscriptome we prefer to have unique ORFs quantified over all samples so comparisons can be made at ORF level. It sounds like you're mostly interested in functional annotation, is that correct? I don't think we have one for prokaryotic genomes (#C0394F86LD9 is for eukaryotes) but it would probably be relatively easy to write one since many tools are used by other nf-core pipelines and available as genomes.

Yes, I am only focusing on functional annotation. Thanks for your rapid response!

As I said, this would be relatively easy to make a pipeline for as we're already using many annotation tools in other pipelines (such as #C02FC6VFQG1). If you feel up to writing a pipeline for this, please head over to #CE6SDEDAA with your idea. You should know that we're a friendly community (in my experience) so you can count on help to get started and solving problems during the coding. Also, check the nf-core homepage for documentation, training etc. Unfortunately, I don't have time to actually write the pipeline right now, but I'll keep in mind that this a pure annotation-pipeline is lacking in nf-core.