8000 Update argNorm's citation to publication in Bioinformatics by Vedanth-Ramji · Pull Request #474 · nf-core/funcscan · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Update argNorm's citation to publication in Bioinformatics #474

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
Open
wants to merge 1 commit into
base: dev
Choose a base branch
from
Open

Update argNorm's citation to publication in Bioinformatics #474

wants to merge 1 commit into from

Conversation

Vedanth-Ramji
Copy link
Contributor

argNorm was recently published in Bioinformatics: https://doi.org/10.1093/bioinformatics/btaf173

The tool has also changed a bit since it was last added as an nf-core module, I'll be working on a few PRs to integrate the latest version with funcscan.

@github-actions GitHub Actions
8000 Copy link

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @Vedanth-Ramji,

It looks like this pull-request is has been made against the Vedanth-Ramji/funcscan master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the Vedanth-Ramji/funcscan dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@Vedanth-Ramji Vedanth-Ramji changed the base branch from master to dev April 18, 2025 17:48
jasmezz
jasmezz requested changes Apr 22, 2025
View reviewed changes
Copy link
Collaborator
@jasmezz jasmezz left a comment

Choose a reason for hiding this comment

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

Congratulations to the accepted paper! 🥳
Just adapt the citation format to the one we use in funcscan, see comment.

CITATIONS.md

> Ugarcina Perovic, S., Ramji, V., Chong, H., Duan, Y., Maguire, F., Coelho, L. P. (2024). argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO). [Preprint] (Unpublished) [DOI: 10.5204/rep.eprints.252448](https://doi.org/10.5204/rep.eprints.252448)
> Svetlana Ugarcina Perovic, Vedanth Ramji, Hui Chong, Yiqian Duan, Finlay Maguire, Luis Pedro Coelho, argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO), Bioinformatics, 2025;, btaf173, https://doi.org/10.1093/bioinformatics/btaf173
Copy link
Collaborator
@jasmezz jasmezz Apr 22, 2025 •
edited
Loading

Choose a reason for hiding this comment

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

Suggested change
> Svetlana Ugarcina Perovic, Vedanth Ramji, Hui Chong, Yiqian Duan, Finlay Maguire, Luis Pedro Coelho, argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO), Bioinformatics, 2025;, btaf173, https://doi.org/10.1093/bioinformatics/btaf173
> Ugarcina Perovic, S., Ramji, V., Chong, H., Duan, Y., Maguire, F., Coelho, L. P. (2025). argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO), Bioinformatics, btaf173. [DOI: 10.1093/bioinformatics/btaf173](https://doi.org/10.1093/bioinformatics/btaf173)

@jfy133
Copy link
Member
jfy133 commented Apr 24, 2025 •
edited
Loading

@Vedanth-Ramji do you want to also update the module itself (if my changes on nf-core/modules was OK )/the pipeline code in this PR to address the structural change you mentioned on slack in this PR?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jasmezz jasmezz jasmezz requested changes

Requested changes must be addressed to merge this pull request.

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

Successfully merging this pull request may close these issues.
3 participants
@Vedanth-Ramji @jfy133 @jasmezz
0