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[REVIEW]: Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance #5397
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
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@mberacochea @rcannood - please let me know if you have any questions about getting started with the reviews. Thanks again! |
@mberacochea @rcannood - I hope that you're having a good weekend. The first step in the review is to create the checklist. Please try to create it using the instructions above. Let me know if you have any difficulties with it. Thanks again! |
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Review checklist for @rcannoodConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@mberacochea - do you have any questions about starting the review? I suggest that you first create a checklist using the command listed above. |
No, that is OK, thanks... I just been busy. |
Review checklist for @mberacocheaConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@mberacochea - how is the review going? Please feel free to leave comments for the author to improve the submission. If you have any questions, please ask me. Thanks again! |
Hey.. apologies this is taking so long. I'll get my review completed before the end of the week. |
@jhayer - how are the revisions going? Please recognize that you'll need to address any issues that are raised by one or both reviewers. So if your team has the capacity to revise the submission to address the open issues, please feel free to do so now. |
Hey, my inital review is done -> jhayer/baargin#26 |
Hi, We addressed most of your comments by several PRs (linked to issues numbers). |
Thank you, @jhayer! I'll let @rcannood and @mberacochea comment here once they get a chance to look at the revisions. |
@rcannood & @mberacochea - please feel free to update us here as you review the changes. Thanks again! |
@rcannood @mberacochea - how are the reviews going? Please feel free to update us in this thread. Thanks again! |
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@jhayer - the manuscript (ie, paper.pdf) looks great! I have no suggestions for improvements, nor did I find any typos. I also can confirm that the hyperlinks in the bibliography direct to the correct target urls. |
@jhayer - there are some issues with the zenodo archive: It looks like the names need reformatting. Please see the above screenshot for a sense of what I see when I click on the link that you've provided. Please fix this and notify me when it's resolved. Thanks again! |
@fboehm - Thanks!! I have now fixed our names on Zenodo. |
@editorialbot set 10.5281/zenodo.8386399 as archive |
Done! archive is now 10.5281/zenodo.8386399 |
@editorialbot set v1.0.0 as version |
Done! version is now v1.0.0 |
@editorialbot recommend-accept |
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👋 @openjournals/bcm-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4700, then you can now move forward with accepting the submission by compiling again with the command |
@jhayer I am the EiC on this track and here to help with final steps. I have checked this review, the paper, the repository, and the archive. Most seems in order. I do have the below points which need your attention.
@misc{Seemann:2022,
author = {Seemann, Torsten},
booktitle = {https://github.com/tseemann/mlst},
mendeley-groups = {Chile_ESBLEcoli},
title = {{MLST: https://github.com/tseemann/mlst}},
year = {2022}
} I would recommend that you alter it to have the URL in a @misc{Seemann:2022,
author = {Seemann, Torsten},
title = {mlst},
year = {2022},
url = "https://github.com/tseemann/mlst"
} |
Thanks, @Kevin-Mattheus-Moerman, for spotting these issues. I'll be sure to look for similar issues in future submissions. |
Thanks @Kevin-Mattheus-Moerman - I have now fixed all the points you listed. |
@editorialbot generate pdf |
@editorialbot accept |
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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘 |
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@jhayer congratulations on this JOSS publication! Thanks for editing @fboehm And a special thanks to the reviewers: @mberacochea, @rcannood |
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Submitting author: @jhayer (Juliette Hayer)
Repository: https://github.com/jhayer/baargin
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @fboehm
Reviewers: @mberacochea, @rcannood
Archive: 10.5281/zenodo.8386399
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@mberacochea & @rcannood, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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Checklists
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