please document haploclique.extra_parameters

[Masterxilo]

under https://github.com/cbg-ethz/V-pipe/wiki/options#haploclique

thanks!

[DrYak]

As you might notice on the disclaimer that wiki page, that page is for the legacy versions of V-pipe (1.00, 2.00 and sars-cov2 branch) as back when Susie published doi:10.1093/bioinformatics/btab015.

The more recent versions of V-pipe (2.99.0, 2.99.1 and master branch) have a full manual of their configuration autogenerated in config/config.html(*), and a short introduction in the README.md of the same directory.

But indeed: @kpj and I have forgotten to run the autogeneration script (utils/create_config_doc). 😅
It's not yet triggered autonomously by github actions.

I'll do it shortly.

---

(*): There's currently a bug in the htmlpreview.github.io servive (CSS file are blocked due to being served with the wrong MIME type) and it's not possible to display the sections of the manual. You have to open it locally.

[DrYak]

config/config.html updated in 02ce515.

There is no change in code, it's only documentation text, you don't need to wait for the docker to finish updating.

[DrYak]

As a side note, I would recommend that you find a similar way to leverage the config schema when you implement the user interface at USZ:
it should be possible to build the option interface using this.

(The people at Sapporo are also thinking out these kind of approaches for their web interface).