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.

Sign up for GitHub

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

Jump to bottom

Added project info to report #197

Merged
merged 9 commits into from
Jan 29, 2024
Merged

Added project info to report #197

merged 9 commits into from
Jan 29, 2024

Conversation

WackerO
Copy link
Collaborator

@WackerO WackerO commented Nov 14, 2023

...and added newline between report author and workflow version. Example report with the new header is attached

SRP254919_contact.html.zip

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions GitHub Actions
Copy link

github-actions bot commented Nov 14, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅

Posted for pipeline commit d62c163

+| ✅ 164 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-27 08:28:39

pinin4fjords
pinin4fjords reviewed Nov 15, 2023
View reviewed changes
assets/differentialabundance_report.Rmd Outdated
@@ -22,6 +22,22 @@ params:
study_abundance_type: NULL
report_file: NULL,
report_title: NULL,
report_pi_name: NULL
Copy link
Member

Choose a reason for hiding this comment

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

Could we just have comma-separated lists please?

@pinin4fjords
Copy link
Member

I also think we should add something to the CSS to place 'contributor blocks' inline, so that we better use the horizontal space.

@WackerO
Copy link
Collaborator Author

WackerO commented Nov 16, 2023 •
edited by pinin4fjords
Loading

You mean so that the different blocks are next to each other? Let me see if I can figure something out

Yes, lots of contributors will use a lot of vertical space. We can fix it by making each contributor an inline div or having them float left, but it will take me a minute to figure out how to do it via the markdown. I can have a go at some point if you can't figure it out.

@WackerO
Copy link
Collaborator Author

WackerO commented Jan 16, 2024 •
edited
Loading

Alright, some changes later: The param --report_contacts_file expects a single TXT file with all the PIs and authors and project managers and whatever. As it is, the TXT file in this zip will produce the report in the same zip:
all_bold.zip

Alternatively, I removed the asterisks from the RMD file and added them directly into the contacts file (see formatted zip). This allows users to add markdown symbols into their contacts to decide themselves how they want that section of the report to be formatted.
I personally find this to be really cool (and as bold/italics can both be done with * characters, it is also fairly simple to use), but of course that would be the "advanced" version and I'm not sure if we should keep this as simple as possible and just print all contacts in bold.
Thoughts? @pinin4fjords
formatted.zip

@pinin4fjords
Copy link
Member

Sorry, but I think this has just got over-complicated- now you have a new file format for the contributors to document and maintain for users, plus the parsing logic.

I suggest something much simpler. A set of parms with comma-separated values:

  • report_contributor_names
  • report_contributor_role (PI, postdoc, bioinformatics engineer)
  • report_contributor_affiliation

Again, don't assume PI, it only makes sense in academia

@WackerO
Copy link
Collaborator Author

WackerO commented Jan 23, 2024

Sorry, but I think this has just got over-complicated- now you have a new file format for the contributors to document and maintain for users, plus the parsing logic.

I suggest something much simpler. A set of parms with comma-separated values:

* report_contributor_names

* report_contributor_role (PI, postdoc, bioinformatics engineer)

* report_contributor_affiliation

Again, don't assume PI, it only makes sense in academia

Done! As discussed, it is now only a single string param; contribs are separated by ;, linebreaks are indicated by \n

@pinin4fjords
Copy link
Member

Also, an example report with this please?

@WackerO
Copy link
Collaborator Author

WackerO commented Jan 24, 2024

Also, an example report with this please?

Sure, here you go!
SRP254919.html.zip

pinin4fjords
pinin4fjords approved these changes Jan 29, 2024
View reviewed changes
Copy link
Member

@pinin4fjords pinin4fjords left a comment

Choose a reason for hiding this comment

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

Looks good now- much more concise. Thanks!

@WackerO WackerO merged commit 6130058 into nf-core:dev Jan 29, 2024
14 checks passed
@WackerO WackerO deleted the project_info branch January 29, 2024 13:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@pinin4fjords pinin4fjords pinin4fjords approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@WackerO @pinin4fjords