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

Introductory workflow + workflow section #501

Merged
merged 25 commits into from
Jul 11, 2024

Conversation

AxelDgn
Copy link
Contributor

@AxelDgn AxelDgn commented May 29, 2024

Currently, OMA chapters focus on individual methods/analyses. In order to simplify and guide its use, here's an introductory workflow for the most basic methods. From importing data to understanding its structure and handling (transformation, subsetting, aggregation,...).

It's not finished yet we still have to add some content.

inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow/Introductory.qmd Outdated Show resolved Hide resolved
inst/assets/book.scss Outdated Show resolved Hide resolved
@TuomasBorman TuomasBorman mentioned this pull request Jun 3, 2024
@antagomir
Copy link
Member

Status of this one?

@AxelDgn
Copy link
Contributor Author

AxelDgn commented Jun 13, 2024

Status of this one?

I'm working on it but I was focused on my internship report, so it's progressing slowly, it'll be done for the next week

inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
Copy link
Contributor

@TuomasBorman TuomasBorman left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Couple of points. I had now time to render this. It looks nice and is probably very useful for many users. Thanks!

inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/pages/images/logo.svg Outdated Show resolved Hide resolved
inst/pages/Introductory-workflow.qmd Outdated Show resolved Hide resolved
inst/assets/book.scss Outdated Show resolved Hide resolved
inst/assets/book.scss Outdated Show resolved Hide resolved
Copy link
Contributor

@TuomasBorman TuomasBorman left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Approvement for the workflow. It's very nice.

I still want comments for the formatting. It should be kept in mind that there will be more workflows in the future. Do they work with this new formatting?

As developing the methods and the content of book take most of our time, we want to rely that the structure and format of book works. That is why we use BiocBook. This format modification is more than welcome, and the already implemented changes in format have already improved OMA.

I want just to make sure that we can maintain this formatting without sudden failures that we cannot solve without extensive amount of work

@antagomir
Copy link
Member

@AxelDgn can we finalize this, seems nearly ready?

@ElySeraidarian
Copy link
Contributor

I have removed the workflow formatting, fixed issues that came with it (e.g. flags not centered anymore). Also fixed some typo issues. Not have gone through all the text but I could check if there are small typo issues

Copy link
Contributor

@TuomasBorman TuomasBorman left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Great! Let's merge this now and improve it later if needed. Thanks all!

@TuomasBorman TuomasBorman merged commit 95903b0 into microbiome:devel Jul 11, 2024
1 check passed
jkc9886 pushed a commit to jkc9886/OMA that referenced this pull request Jul 25, 2024
Co-authored-by: Insaynoah <[email protected]>
Co-authored-by: Tuomas Borman <[email protected]>
Co-authored-by: Leo Lahti <[email protected]>
Co-authored-by: seraidarian <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

5 participants