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bio-raum / FooDMe2

A nextflow pipeline for the identification of species from mixed samples based on mitochondrial amplicons
https://bio-raum.github.io/FooDMe2/
GNU General Public License v3.0
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[Improvement] Doc improvement #57

Closed gregdenay closed 1 month ago

gregdenay commented 1 month ago
marchoeppner commented 1 month ago

Just as a reminder to us, we should probably remove any mentioning of support for ONT/Pacbio/Torrent for the time being. This will only confuse people.

gregdenay commented 1 month ago

I removed mentions of ONT for now. I polished things a bit and forced the doc deployment from the dev branch. There is still room for improvements but it looks fine.

Do you see the need for additional changes on the form and/or content?

gregdenay commented 1 month ago

Ah and images have to be packed under docs/img/ otherwise it's a mess to access them from the doc

marchoeppner commented 1 month ago

Right, so I am just listing things to make sure I am not accidentally breaking your nice documentation ;) Looks really great now.

gregdenay commented 1 month ago

Links fixed (for the record they should be relative paths from the current file, NOT from the doc root) I removed the sequencing technology section of Usage doc

I'll try to implement doc versionning with mike.

We should update the dag diagram but it already looks kind of crazy. Maybe we could put a fancy subway plan style diagram like in the nf-core pipeline? What do you think?

marchoeppner commented 1 month ago

The subway-style diagrams in nf-core are hand-made in Illustrator or something like that - so yes, doable, but ...any volunteers? ;) In any case, not absolutely necessary for the 1.0 target, I suppose.

gregdenay commented 1 month ago

https://github.com/bio-raum/FooDMe2/blob/dev/docs/img/pipeline_dag.png

marchoeppner commented 1 month ago

Just noticed that the FooDMe paper isn't referenced anywhere. Probably something you would want to add? I mean, it is still "FooDMe", so short of us writing this up already as a follow-up or application note, it makes sense to at least cite the original paper.

gregdenay commented 1 month ago

Versionning is working. Note that the url must be bio-raum.github.io/FooDMe2/latest

marchoeppner commented 1 month ago

Very nice! Any idea why the "latest" version isn't showing the logo?

marchoeppner commented 1 month ago

Nevermind, you haven't merged dev into main yet.

marchoeppner commented 1 month ago

The troubleshooting link is dead (typo, I am guessing): https://bio-raum.github.io/FooDMe2/latest/toobleshooting.md

Same with the pipeline link: https://bio-raum.github.io/FooDMe2/latest/piepline.md

gregdenay commented 1 month ago

I switched the doc build to a strict mode so that the github action will should on missing links and documents. Fixed the links. Favicon is now displaying correctly (dev doc).

That's all I had on my list. Do you still have changes for the doc?

gregdenay commented 1 month ago

Ha nevermind still need to build a redirect from https://bio-raum.github.io/FooDMe2 to https://bio-raum.github.io/FooDMe2/latest, no diea why mike didn't do it

marchoeppner commented 1 month ago

Looks good on the dev branch, maybe best to do a pr into main to see if everything transfers ok. And then do a final check of everything (incl. docs) - and if that all looks good, do the 1.0 release.

gregdenay commented 1 month ago

It set it up so that the 'latest' doc is only replaced on release, that should happen automatically (tested yesterday with 1.0.0.alpha.2). I'll open a PR