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

[REVIEW]: Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance #5397

Closed
editorialbot opened this issue Apr 22, 2023 · 75 comments
Assignees
Labels
accepted Nextflow published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Apr 22, 2023

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

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2"><img src="https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2/status.svg)](https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2)

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

@editorialbot editorialbot added Nextflow Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Apr 22, 2023
@editorialbot
Copy link
Collaborator Author

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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (340.0 files/s, 50197.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            180            230            797
Markdown                         2            114              0            385
TeX                              1             16              0            292
YAML                             3              5              9             39
-------------------------------------------------------------------------------
SUM:                            14            315            239           1513
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 1231

@editorialbot
Copy link
Collaborator Author

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
- 10.1093/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
Copy link
Collaborator Author

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@fboehm
Copy link

fboehm commented Apr 25, 2023

@mberacochea @rcannood - please let me know if you have any questions about getting started with the reviews. Thanks again!

@fboehm
Copy link

fboehm commented Apr 30, 2023

@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!

@rcannood
Copy link

rcannood commented May 1, 2023

👍

@rcannood
Copy link

rcannood commented May 1, 2023

Review checklist for @rcannood

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/jhayer/baargin?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@jhayer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@fboehm
Copy link

fboehm commented May 9, 2023

@mberacochea - do you have any questions about starting the review? I suggest that you first create a checklist using the command listed above.

@mberacochea
Copy link

@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.

@mberacochea
Copy link

mberacochea commented May 11, 2023

Review checklist for @mberacochea

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/jhayer/baargin?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@jhayer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@fboehm
Copy link

fboehm commented May 23, 2023

@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!

@mberacochea
Copy link

@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.

@fboehm
Copy link

fboehm commented May 24, 2023

@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.

@jhayer
Copy link

jhayer commented May 26, 2023

@fboehm - Thank you it's ongoing (slowly, also a bit busy ATM). We are making PRs for addressing each comment from @rcannood

@mberacochea
Copy link

Hey, my inital review is done -> jhayer/baargin#26

@jhayer
Copy link

jhayer commented Jun 15, 2023

Hi, We addressed most of your comments by several PRs (linked to issues numbers).
We would like to merge all the PRs before proceeding with the remaining issues (tests: issues #47 and #48, and release: #44).
Could you please @rcannood and @mberacochea check that all this is ok before we merge?
Thank you !

@fboehm
Copy link

fboehm commented Jun 16, 2023

Thank you, @jhayer! I'll let @rcannood and @mberacochea comment here once they get a chance to look at the revisions.

@fboehm
Copy link

fboehm commented Jun 22, 2023

@rcannood & @mberacochea - please feel free to update us here as you review the changes. Thanks again!

@fboehm
Copy link

fboehm commented Jun 29, 2023

@rcannood @mberacochea - how are the reviews going? Please feel free to update us in this thread. Thanks again!

@editorialbot
Copy link
Collaborator Author

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
Copy link

fboehm commented Oct 14, 2023

@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
Copy link

fboehm commented Oct 14, 2023

@jhayer - there are some issues with the zenodo archive:

image

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
Copy link

jhayer commented Oct 16, 2023

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

@fboehm
Copy link

fboehm commented Oct 17, 2023

@editorialbot set 10.5281/zenodo.8386399 as archive

@editorialbot
Copy link
Collaborator Author

Done! archive is now 10.5281/zenodo.8386399

@fboehm
Copy link

fboehm commented Oct 17, 2023

@editorialbot set v1.0.0 as version

@editorialbot
Copy link
Collaborator Author

Done! version is now v1.0.0

@fboehm
Copy link

fboehm commented Oct 17, 2023

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author

Attempting dry run of processing paper acceptance...

@editorialbot
Copy link
Collaborator Author

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
Copy link
Collaborator Author

👋 @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 @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 17, 2023
@Kevin-Mattheus-Moerman
Copy link
Member

Kevin-Mattheus-Moerman commented Oct 18, 2023

@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"
}

@fboehm
Copy link

fboehm commented Oct 18, 2023

@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
Copy link

jhayer commented Oct 19, 2023

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

@Kevin-Mattheus-Moerman
Copy link
Member

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@Kevin-Mattheus-Moerman
Copy link
Member

@editorialbot accept

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

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
Copy link
Collaborator Author

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

@editorialbot
Copy link
Collaborator Author

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

Here's what you must now do:

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

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Oct 19, 2023
@Kevin-Mattheus-Moerman
Copy link
Member

@jhayer congratulations on this JOSS publication!

Thanks for editing @fboehm

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

@editorialbot
Copy link
Collaborator Author

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05397/status.svg)](https://doi.org/10.21105/joss.05397)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05397">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05397/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05397/status.svg
   :target: https://doi.org/10.21105/joss.05397

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
accepted Nextflow published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials
Projects
None yet
Development

No branches or pull requests

6 participants