Hi everyone, First of all thank you for the nf-core teams for making these pipelines. I find them very pedagogical which is nice for beginners like me 🐣. My question is on the gtdb_min_completeness and max_contamination. I'm using the 5.1.0 version and looking at the nextflow_schema.json file, i see these parameters are based on the Busco analysis. I was wondering if it was possible to change this to base the min completeness and max contamination evaluation on another binqc_tool, like checkm2 ? Sorry if that question was answered already, I couldn't find it on the github issues or in this slack canal.

Hi Simon, More recent versions of mag supports this :)

I think that's how we ended up implementing it, yeah

Thanks for confirming, I'll make an issue to update the docs

I think also though that previously we did use the CheckM/CheckM2/BUSCO score, depending on what tool was actually selected?

I don't remembe rnow 😅 possibly

Hello, thank you for your answers ! I didn't try running gtdb after checkm2 based on the documentation but I'll try it and see if it works !