We -- me and Claude -- think it's time for 0.9.4 or 0.10.0 -- including a new Bioconda recipe -- what do you think @auguste.gardette? (The bioconda automated PR is apparently not for the latest commit.) We would then base the nf-core modules and subworkflow on that.

Hi @Daniel Lundin, I just read your message. What about 1.0.0? EPA-ng and the staged interface make this a different tool rather than a patch to upstream. A 1.0.0 release would also indicate that the

--stage

interface is stable enough for you to pin your modules against. Maybe one question before that: I’d be curious to hear feedback from @Donovan Parks on his run with the 16S sequences. Maybe we need to fix other things ?

I proposed that to Claude and it suggested no, thinking that the few things we found yesterday were an indication that there were more things to find. And your question to Donovan relates to that too. We don't have to decide today, the nf-core modules we write are circumventing what we found yesterday and could remain as they are until we're fairly confident that it's time for a 1.0.0, i.e. no urgent need for a 0.9.4 either.

I think I'll ask Sofoklis from MetaPlantcode also to test it too, if he's interested, to get more feedback on the tool

Absolutely. We should tell him about the pipeline (#C0BVDK00QKY) too. I'm working on it.