Hi Benji! Thanks for the interest and ideas! Is your idea to contribute to the pipeline or work just on your fork (I can't tell from some of your phrasing e.g. 'replacing' antiSMASH) Regardless, I think conceptually there is no reason why we should not support organisms outside of prokaryotes Without me having any experience of plantiSMASH and skimming the website/docs/github: We wouldn't skip number 3 as we would still need to annotate the genomes (just with different tools), so we would just add another annotation option but that is easy. We don't have have to replace antiSMASH - just have an additional option. It could be comBGC reporting might be difficult as I imagine there might be different metrics, but we don't have to support all tools in comBGC (e.g. HMMsearch isn't represented in that, for example) Technically one blocker is that plantiSMASH is not currently on bioconda, but it looks like the developers would be amenable, and it should be easy to make a recipe given the tool is on pypi.

Hi James! Thank you for such a thoughtful response! I’d be very happy to help contribute that change, but my background with bioinformatics workflows has primarily been in Snakemake not Nextflow, so it will definitely be somewhat of a learning curve there at least. I tried making a Snakemake workflow for plantiSMASH based on funcscan, but I gave up quickly since I thought just learning Nextflow and maybe helping to contribute this would be more beneficial in the long run for myself and others

We are more than happy to help upskill you to be able to learn Nextflow 🙂 We have a weekly helpdesk, but I also run different dev sessions for pipelines I'm working on. Funcscan not currently because it was just me (@Jasmin Frangenberg is in the middle of switching jobs), but I could resurrect it. Looking at your timezone of your profile I guess you're normally based in the the americas?

Yeah I’m on the east coast of the US, but I’m pretty flexible with my hours so I can try to do what works best for you as much as possible