Finally got round to a new release: https://github.com/pinin4fjords/nf-metro/releases/tag/0.7.0 Loads of bugfixes, plus lots of work to try and make the layout engine more robust

I will play around with it soon, thanks @Jonathan Manning

It still has a tendency of breaking in unanticipated scenarios, Sarek will be the ultimate challenge!

Sarek is the ultimate challenge for most things

Do you just create your mermaid file manually? I’m a bit confused on how best to go about starting to generate the mermaid diagram with the potential routes through a pipeline

You can actually do a Nextflow import for simple stuff (https://pinin4fjords.github.io/nf-metro/latest/nextflow/), but it's not very good where the conceptual flow is very different from the literal one (if that makes sense). I did write a Claude skill to help, if that's useful: https://github.com/pinin4fjords/nf-metro/blob/main/.claude/skills/pipeline-metro-diagram/SKILL.md

Hmm yeah I took one look at my nextflow generated mmd and decided that wouldn't work - thousands of nodes and connections and lots of small processes (think VCF indexing etc) which aren't important to the conceptual flow. I actually have a mmd I handcrafted today but it's generating a very borked SVG which I am not sure if I can fix or it's a fundamental issue with my flow

It is still a bit temperamental, turns out layout is hard to automate! If you post an issue with the mmd and the render I'll try to fix the issues and make it work for the next release.

Ok thanks, I wasn't sure what the best avenue for help on that would be. I would also point out that your variantbenchmarking example in the docs looks great, but the mmd on github won't render (on github) and the png looks borked

The ones in the docs are auto-generated from code so should represent the 'real' situation, but I'll double check. The static png renders may have snuck in at some point. I don't expect GitHub to render these well

So it's the static png on GitHub that looks weird - different to the docs. And the mermaid for it just doesn't render at all.

yeah, I get it, I'm saying I think the png is a relic committed by mistake. And it's kind of a modified mermaid, so not surprised GitHub isn't rendering the mmds.