I finally made a metro map for nf-core/ampliseq. Its simplified regarding modules and connections to rather highlight options and capabilities but also attempting to advance understanding of the pipeline concept. Not sure if I made the right choices, so I would appreciate feedback. Potential issues that I saw but accepted as simplification: • ONT & Illumina both default • crossover ONT to Illumina (theoretically, someone could set for Illumina data Savont, or for ONT data DADA2, but would need explicit overwriting) • DADA2 steps heavily simplified • every single step is optional. One of DADA2 and Savont must run when raw reads are input. With ASV intermediate input, even those are omitted. However, ASV input isnt shown because most downstream stuff isnt compatible then (no abundance profile!). So I opted not to loop around optional steps.

That looks really good! I think it's very clean and easy to follow.

Thanks for the feedback! > nf-metro? Yes, total mess with connectors, I didnt made it to work the way I wanted. 😬

Overall I like it a lot. I think the simpifications are a necessary step to "metrofy" a pipeline. I also find it very tempting to be as accurate as possible, but I guess these maps should give you an idea where it is going, similar to how metro-maps of cities also do not accurately preserve the spacial relationships. Here are some comments: • I would reconsider if the 4 lines going into the reporting "station" are really helpful, or if this would be equally nice it it was just text + node. • The

purple

extraction line, is not part of the legend. • What exactly does

Limited

(flower-shape) mean? • Do you really need the mutually exclusive shape, which you only use once, for something that seems very specific to me (ITSx vs ITSxRust?) and may not need to be displayed on the map? • While the numbering is generally fine, I am not sure how I feel about having 8 between 5 and 6. • The grey backgrounds are not well aligned on the bottom (some stick out more), which some people get very annoyed by 😉

All good points, thanks! I think most I can solve. The "Limited" is also a simplification: only some taxonomic references (3) can have an "extraction" with primers, and only DADA2 (but more to come) taxonomic classifications (4) can be "consolidated". Additionally, each taxonomic classifier (4) has only a subset of taxonomic references (3) but with more or less large overlaps. It would add a lot of noise to the figure to add that info. Thats in the usage docs though. Maybe I should add a small figure caption that mentions the largest simplifications...

Yeah, I think this should come with a limited* *(check docs) or something

Added purple line, Limited*** (will add figure caption), background alignment, picrust2 routing (fixed mistake), Limited***, changed numbering. Did not change "Mutually exclusive" ITSx/ITSxRust (this is impactful because they are optimized for different data), kept "Reporting" lines (because otherwise its colorless, didnt like it):

hyper pedantic comment: I think it is either

R Markdown

or

rmarkdown

Ace! Please add it to your pipeline config when you commit it to the repo 🙂 (new thing) nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#…

PR: github.com/nf-core/ampliseq/pull/1087