Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add docs for different config profiles #6

Open
10 tasks done
drpatelh opened this issue Nov 26, 2018 · 20 comments
Open
10 tasks done

Add docs for different config profiles #6

drpatelh opened this issue Nov 26, 2018 · 20 comments

Comments

@drpatelh
Copy link
Member

drpatelh commented Nov 26, 2018

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:

  • BINAC (Alex P)
  • CCGA
  • CFC (Alex P)
  • GIS
  • hebbe
  • phoenix (Alex P)
  • uct_hex
  • uppmax_devel
  • uppmax
  • uzh (Alex P)
@apeltzer
Copy link
Member

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

@drpatelh
Copy link
Member Author

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
Copy link
Member

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
Copy link
Member

ewels commented Nov 27, 2018

@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 ewels transferred this issue from nf-core/tools Nov 27, 2018
@ewels
Copy link
Member

ewels commented Nov 27, 2018

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

@ewels ewels changed the title Provide central location for documentation of custom Institutional configs Add docs for different config profiles Nov 27, 2018
@ewels
Copy link
Member

ewels commented Nov 27, 2018

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
Copy link
Member Author

I have added the docs for the Crick in the nf-core/configs/docs/ folder. See #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
Copy link
Member

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
Copy link
Member Author

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
Copy link
Member

matq007 commented Jan 14, 2019

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.

@nf-core nf-core deleted a comment from apeltzer Mar 14, 2019
@ewels
Copy link
Member

ewels commented Mar 14, 2019

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
Copy link

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?

jfy133 added a commit that referenced this issue Dec 5, 2019
@ewels ewels moved this to Todo in Hackathon-March-2022 Mar 1, 2022
@ajodeh-juma ajodeh-juma moved this from Todo to In Progress in Hackathon-March-2022 Mar 18, 2022
@ajodeh-juma ajodeh-juma moved this from In Progress to Needs Review in Hackathon-March-2022 Mar 18, 2022
@ggabernet ggabernet moved this from Needs Review to Todo in Hackathon-March-2022 Mar 18, 2022
@abhi18av
Copy link
Member

abhi18av commented Oct 10, 2022

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

  • cfc_dev.config
  • crg.config
  • gis.config
  • 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

ameynert pushed a commit that referenced this issue Oct 26, 2022
Merge base repository into fork
@maxulysse
Copy link
Member

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
Copy link
Member

apeltzer commented Mar 1, 2023

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

@maxulysse
Copy link
Member

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
Copy link

yassineS commented Mar 2, 2023

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
Copy link
Member

jfy133 commented Mar 2, 2023

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

@FriederikeHanssen
Copy link
Contributor

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

@aelezi01 aelezi01 moved this from Todo to In Progress in nf-core Hackathon March 2023 Mar 28, 2023
@aelezi01 aelezi01 assigned aelezi01 and unassigned aelezi01 Mar 28, 2023
@aelezi01 aelezi01 moved this from In Progress to Todo in nf-core Hackathon March 2023 Mar 28, 2023
@mihai-sysbio
Copy link

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).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
No open projects
Development

No branches or pull requests