Add docs for different config profiles

[drpatelh]

Custom configs are now hosted centrally at nf-core/configs. We need to think about where we host the documentation for running these config files. These are currently added on a per-pipeline basis but it would be good to also host them centrally so they are available to all pipelines.

This will also probably involve refactoring the current docs to deal with this.

Documention to-do list:

• [x] BINAC (Alex P)
• [x] CCGA
• [x] CFC (Alex P)
• [x] GIS
• [x] hebbe
• [x] phoenix (Alex P)
• [x] uct_hex
• [x] uppmax_devel
• [x] uppmax
• [x] uzh (Alex P)

[apeltzer]

How about storing these centrally here together with the configs and simply refer to this repository, explaining why these are kept separately ?

[drpatelh]

Thats what I was thinking. So we can put them in nf-core/configs/docs/configuration/? Thats where they are currently kept for other pipelines.

If someone decides to add a custom config how much do we push to provide documentation too? It would be nice to have one per custom config but do we expect everyone to be able to write a markdown document? Maybe we provide a template in nf-core/configs and document that?

[apeltzer]

Yes, sounds good.

I would think writing Markdown is pretty easy these days (even online WYSIWYG editors exist), so why not push for writing some basic lines describing the config then?

[ewels]

@apeltzer:

How about storing these centrally here together with the configs and simply refer to this repository, explaining why these are kept separately ?

This issue that we're commenting on here is on tools - I'm guessing you mean on the configs repository?

[ewels]

I moved the issue from tools to configs 🎉 (thanks, new GitHub feature)

[ewels]

Note that I think nf-core/configs/docs/ would be fine for organisation. Could have a TEMPLATE.md if we really want? Or people can just look at the existing files.

[drpatelh]

I have added the docs for the Crick in the nf-core/configs/docs/ folder. See https://github.com/nf-core/configs/pull/7

We need to add docs for the rest of the configs currently hosted in the repository for consistency.

Also, need to reference the documentation for these profiles in nf-core/tools template. This is what we have so far: https://github.com/nf-core/tools/blob/dev/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/docs/usage.md#custom-resource-requests

Im not sure whether its possible to get a dynamic listing of all the available profiles available to use when running the pipeline but that would be quite neat.

[apeltzer]

Neat! Something like a git submodule that we integrate into the nf-core/tools package maybe? Not been using these too often, but it might be possible.

[drpatelh]

Thanks @apeltzer!

I was thinking it would be nice if we could maybe automatically add the list of available profiles to the help string produced by the pipeline. Maybe we can add an extra description document in nf-core/configs that contains the profile name and a brief help comment. This can then be parsed in nextflow.config and rendered in the help.

I'm not sure if nextflow currently checks that the name of the profile has to be valid. I'll test that.

[matq007]

It would be super cool to maybe specify a little more how to use this config files in an existing/new nfcore solution. @apeltzer has a really nice code in nextflow.config.

[ewels]

Deleted your comment @apeltzer and added the list to the original post by @drpatelh so that we get a nice completion tick-list on the issues page.

[mihai-sysbio]

For Uppmax #53 and Hebbe #54 the CI seems to report the same issue. Is there a mismatch between the documentation and the changes in the PRs?

[abhi18av]

Considering that the list in the first comment is now completed already I am adding a list of configs (from https://github.com/nf-core/configs/tree/master/conf) which need to be documented still

• [x] cfc_dev.config
• [x] crg.config
• [x] gis.config
• [x] hebbe.config
• [ ] phoenix.config

Here's the template.md which can be used to create the docs for configs above.

EDIT by @maxulysse update list of missing docs

[maxulysse]

Friendly reminder:

@FriederikeHanssen we're missing docs for the cfc_dev config @athbaltzis we're missing docs for the crg config @ewels we're missing docs for the hebbe config @yassineS and @apeltzer we're missing docs for the phoenix config

[apeltzer]

Yeah thats one for @yassineS - can't work on this at the moment unforrtunately as I'm not even near that cluster ;-)

[maxulysse]

Yeah thats one for @yassineS - can't work on this at the moment unforrtunately as I'm not even near that cluster ;-)

You're still listed as contact in the config, that's how I found you

[yassineS]

The cluster has been replaced by a new one, hpc1, but I will let @roberta-davidson comment. She is our resident expert now on all eager matters.

[jfy133]

Let me know if you need any advice/help @roberta-davidson!

[FriederikeHanssen]

added in #470 , also cleaned up the -profile cfc docs

[mihai-sysbio]

Considering that the list in the first comment is now completed already I am adding a list of configs (from https://github.com/nf-core/configs/tree/master/conf) which need to be documented still

The list should be edited to replace hebbe by vera (docs).