(although it looks like it's abandoned...)

Might be good reasons why it’s abandoned. An all-in-one ‘any organism’ annotation pipeline is very hard to keep up to date.

Yeah, I guess we would either need to constrain it to either two types of organisms or the target biomolecule/gene (so to say)

a subworkflow would make sense

That sounds great to me! That’s kinda why I initially mentioned a fork since I wasn’t sure integrating the plant logic directly into funcscan made sense

Yeah a fork makes sense to me as well

Could be worth reaching out to the plantiSMASH/fungiSMASH authors though if they have any interest in helping to maintain that functionality if it was added to funcscan. I noticed in researching for this project I’m working on that I couldn’t find a single comprehensive pipeline using anything but antiSMASH

Do you mean if they want to maintain the various *smash implementations? Or making the implementations available (conda, docker, etc)? My impression from talking to Kai about this years ago was they want to make it easily accessible and deployable, but going beyond that really depends on the maintenance burden

I was just thinking it could be in the interest of the *smash authors to help maintain the integration of those tools with funcscan so users can more readily use the various *smash implementations. Could totally be out of scope of what they want to do in terms of increasing their maintenance burden, but I just thought it was worth mentioning as an idea

Something like having an ‘official’ set of nf-core modules for this, with associated containers/conda packages?

Yeah that’s pretty much what I was thinking. I’m fairly new to the nf-core ecosystem myself, so sorry if I didn’t explain myself well

My guess is you likely want this b/c you need (or would really like) the functionality, I think you mentioned having a need for a plant project. So, if I were in the same position I’d first develop those modules, and maybe the associated subworkflows, so you can get your work done. “First implementation wins”

Sorry guys, it was putting to kids bed during your back and forth. I think it sounds reasonable then to make a subworkflow but not necessarily integrate it into funcscan due the complexity. Then you can make a fork or just a much more minimal custom pipeline(s) for whatever*smash tools you want to run. I honestly think it's very unlikely the fungi/plantSMASH Devs will want to maintain the nf-core modules themselves (I'm sure they already have to maintain a lot of other things like pypi/Conda recipes and so forth) - but you could ask! I'm basing this off of previous reluctance of the antiSMASH devs to properly support bioconda/biocontainer recipes/images (Because they build their own images which is sort of fair, but not how we do things in nf-core really). That said is not _that_hard to make an nf-core module that other people can also make/make one.

Yep I agree on basically all of these points. I’d say the majority of open-source developers aren’t directly involved with downstream deployment of their tools unless they write them directly, esp if it’s ecosystem-specific (like your comment ‘not how we do things in nf-core really’).

Exactly