[REVIEW]: Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jhayer@fboehm<!--end-editor-- Reviewers: @mberacochea, @rcannood Archive: 10.5281/zenodo.8386399

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@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. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fboehm know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @rcannood

📝 Checklist for @mberacochea

fboehm commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/D41586-022-00228-X is OK
- 10.1038/nbt.3820 is OK
- 10.1128/mSystems.00190-20 is OK
- 10.1093/BIOINFORMATICS/BTY560 is OK
- 10.1002/CPBI.102 is OK
- 10.1371/JOURNAL.PCBI.1005595 is OK
- 10.1186/S13059-019-1891-0 is OK
- 10.1038/S41596-022-00738-Y is OK
- 10.1093/BIOINFORMATICS/BTT086 is OK
- 10.1093/MOLBEV/MSAB199 is OK
- 10.1128/AAC.02412-14 is OK
- 10.1099/MGEN.0.000398 is OK
- 10.1093/NAR/GKAC920 is OK
- 10.1038/s41598-021-91456-0 is OK
- 10.1093/BIOINFORMATICS/BTU153 is OK
- 10.1099/MGEN.0.000685 is OK
- 10.1093/BIOINFORMATICS/BTV421 is OK

MISSING DOIs

- None

INVALID DOIs

- None

fboehm commented 11 months ago

@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.

fboehm commented 11 months ago

@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!

jhayer commented 11 months ago

@fboehm - Thanks!! I have now fixed our names on Zenodo.

fboehm commented 11 months ago

@editorialbot set 10.5281/zenodo.8386399 as archive

editorialbot commented 11 months ago

Done! archive is now 10.5281/zenodo.8386399

fboehm commented 11 months ago

@editorialbot set v1.0.0 as version

editorialbot commented 11 months ago

Done! version is now v1.0.0

fboehm commented 11 months ago

@editorialbot recommend-accept

editorialbot commented 11 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 11 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/D41586-022-00228-X is OK
- 10.1038/nbt.3820 is OK
- 10.1128/mSystems.00190-20 is OK
- 10.1093/BIOINFORMATICS/BTY560 is OK
- 10.1002/CPBI.102 is OK
- 10.1371/JOURNAL.PCBI.1005595 is OK
- 10.1186/S13059-019-1891-0 is OK
- 10.1038/S41596-022-00738-Y is OK
- 10.1093/BIOINFORMATICS/BTT086 is OK
- 10.1093/MOLBEV/MSAB199 is OK
- 10.1128/AAC.02412-14 is OK
- 10.1099/MGEN.0.000398 is OK
- 10.1093/NAR/GKAC920 is OK
- 10.1038/s41598-021-91456-0 is OK
- 10.1093/BIOINFORMATICS/BTU153 is OK
- 10.1099/MGEN.0.000685 is OK
- 10.1093/BIOINFORMATICS/BTV421 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 11 months ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4700, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 11 months ago

@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.

[x] Please amend the version tag listed on your archive link to match v1.0.0, it currently says v1
[x] Your text features British English (e.g. analysed and customise) as well as American English (e.g. standardize, parallelize, and summarize), please amend so you consistently use one.
[x] Check if ...using MLST tool... should be rewritten as ...using the MLST tool...
[x] Currently you have cited a URL using the following .bib file entry:

@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 url field so it renders properly in the references (note I also fixed the title).

@misc{Seemann:2022,
author = {Seemann, Torsten},
title = {mlst},
year = {2022},
url = "https://github.com/tseemann/mlst"
}

fboehm commented 11 months ago

@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.

[ ] Please amend the version tag listed on your archive link to match v1.0.0, it currently says v1

[ ] Your text features British English (e.g. analysed and customise) as well as American English (e.g. standardize, parallelize, and summarize), please amend so you consistently use one.

[ ] Check if ...using MLST tool... should be rewritten as ...using the MLST tool...

[ ] Currently you have cited a URL using the following .bib file entry:
@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 url field so it renders properly in the references (note I also fixed the title).
@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.

jhayer commented 11 months ago

Thanks @Kevin-Mattheus-Moerman - I have now fixed all the points you listed.

Kevin-Mattheus-Moerman commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 11 months ago

@editorialbot accept

editorialbot commented 11 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 11 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Hayer given-names: Juliette orcid: "https://orcid.org/0000-0003-4899-9637" - family-names: Dainat given-names: Jacques orcid: "https://orcid.org/0000-0002-6629-0173" - family-names: Marcy given-names: Ella orcid: "https://orcid.org/0009-0002-6000-1665" - family-names: Bañuls given-names: Anne-Laure orcid: "https://orcid.org/0000-0002-2106-8667" contact: - family-names: Hayer given-names: Juliette orcid: "https://orcid.org/0000-0003-4899-9637" doi: 10.5281/zenodo.8386399 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Hayer given-names: Juliette orcid: "https://orcid.org/0000-0003-4899-9637" - family-names: Dainat given-names: Jacques orcid: "https://orcid.org/0000-0002-6629-0173" - family-names: Marcy given-names: Ella orcid: "https://orcid.org/0009-0002-6000-1665" - family-names: Bañuls given-names: Anne-Laure orcid: "https://orcid.org/0000-0002-2106-8667" date-published: 2023-10-19 doi: 10.21105/joss.05397 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 5397 title: "Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05397" volume: 8 title: "Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 11 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 11 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4705
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05397
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 11 months ago

@jhayer congratulations on this JOSS publication!

Thanks for editing @fboehm

And a special thanks to the reviewers: @mberacochea, @rcannood

editorialbot commented 11 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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