[REVIEW]: Snk: A Snakemake CLI and Workflow Management System

[editorialbot]

Submitting author: @Wytamma (Wytamma Wirth)
Repository: https://github.com/Wytamma/snk
Branch with paper.md (empty if default branch):
Version: v0.31.0
Editor: @danielskatz
Reviewers: @huddlej, @beardymcjohnface
Archive: 10.5281/zenodo.14214901

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e0b3241a56503fc2cae712d95c9142d8"><img src="https://joss.theoj.org/papers/e0b3241a56503fc2cae712d95c9142d8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e0b3241a56503fc2cae712d95c9142d8/status.svg)](https://joss.theoj.org/papers/e0b3241a56503fc2cae712d95c9142d8)

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

@huddlej & @beardymcjohnface, 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 @danielskatz 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 @huddlej

📝 Checklist for @beardymcjohnface

[editorialbot]

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

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[editorialbot]

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

✅ OK DOIs

- 10.1186/s12864-022-08358-2 is OK
- 10.1371/journal.pcbi.1010705 is OK
- 10.12688/f1000research.29032.2 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1824.4 files/s, 136829.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        16            470              0           1178
Python                          14            216            335            863
YAML                            13             19             18            276
TOML                             1             13              4             71
TeX                              1              2              0             41
Bourne Shell                     2              2              2             15
-------------------------------------------------------------------------------
SUM:                            47            722            359           2444
-------------------------------------------------------------------------------

Commit count by author:

   506	Wytamma Wirth
     7	Robert Turnbull
     1	Katherine Eaton

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 993

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[danielskatz]

@huddlej & @beardymcjohnface - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7410 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

[huddlej]

Review checklist for @huddlej

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/Wytamma/snk?
  • Yes, but the majority of the source code is in a sibling repository at https://github.com/Wytamma/snk-cli
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Wytamma) 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?

[beardymcjohnface]

Review checklist for @beardymcjohnface

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/Wytamma/snk?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Wytamma) 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?

[huddlej]

@danielskatz @Wytamma I'm finished reviewing the paper and software. It was a pleasure to try out this new tool. There are many times in the last decade that I wish I had had a tool like this; it would have made life easier for me and users of my workflows!

I've opened a few minor issues in the project's repo (linked above) which I'm happy to chat with you about, @Wytamma, if you like.

[danielskatz]

Thanks @huddlej - I assume from the fact that you checked everything off on your list that these issues are not ones that you think need to be addressed for the submission to be published? If this is incorrect, please help me understand which issues do need to be addressed before publication.

[huddlej]

@danielskatz Thank you for checking! I would like the open issues to be addressed before publication, even if they are addressed with a comment that they are out of scope. I'll leave the "Functionality documentation" item unchecked in my list above until then.

[beardymcjohnface]

This package and the idea of the snk.yaml is exactly what I've wanted to make for a while now, so I'm really happy that someone else did it and I don't have to! I would love to see this evolve into something like nf-core but for snakemake.

[danielskatz]

👋 @beardymcjohnface - I assume from your completed checklist that you are also ready for this to be accepted and published, but would like you to confirm this.

[beardymcjohnface]

👋 @beardymcjohnface - I assume from your completed checklist that you are also ready for this to be accepted and published, but would like you to confirm this.

Yes, all good here.

[danielskatz]

👋 @Wytamma - At this point could you:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with proofreading and then accepting the submission. There's a reasonable chance I will ask for changes, but they do not need to be included in the archived software, as the paper itself will be archived as well.

[danielskatz]

👋 @Wytamma - note that this is waiting on you, and is basically ready to go.

I'll go ahead and do the proofreading now to try to reduce the need for future changes.

[danielskatz]

👋 @Wytamma - My suggested changes are in Wytamma/snk#95 - please merge this before the 4 steps mentioned earlier, or let me know what you disagree with.

[Wytamma]

Thanks @danielskatz! I've merged your suggested changes and made a release joss-publication-release. I uploaded the release file to Zenodo and have the DOI 10.5281/zenodo.14214901.

[danielskatz]

@editorialbot set 10.5281/zenodo.14214901 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.14214901

[danielskatz]

@editorialbot set v0.31.0 as version

[editorialbot]

Done! version is now v0.31.0

[danielskatz]

@editorialbot recommend-accept

@Wytamma - please proofread the draft this generates and let me know if it looks ok. I will do the same.

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.1186/s12864-022-08358-2 is OK
- 10.1371/journal.pcbi.1010705 is OK
- 10.12688/f1000research.29032.2 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#6182, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Wytamma]

@editorialbot generate pdf

I added a few minor changes.

[editorialbot]

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

[Wytamma]

@danielskatz Looks good to me 👍

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Wirth
  given-names: Wytamma
  orcid: "https://orcid.org/0000-0001-7070-0078"
- family-names: Mutch
  given-names: Simon
  orcid: "https://orcid.org/0000-0002-3166-4614"
- family-names: Turnbull
  given-names: Robert
  orcid: "https://orcid.org/0000-0003-1274-6750"
doi: 10.5281/zenodo.14214901
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wirth
    given-names: Wytamma
    orcid: "https://orcid.org/0000-0001-7070-0078"
  - family-names: Mutch
    given-names: Simon
    orcid: "https://orcid.org/0000-0002-3166-4614"
  - family-names: Turnbull
    given-names: Robert
    orcid: "https://orcid.org/0000-0003-1274-6750"
  date-published: 2024-11-25
  doi: 10.21105/joss.07410
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7410
  title: "Snk: A Snakemake CLI and Workflow Management System"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07410"
  volume: 9
title: "Snk: A Snakemake CLI and Workflow Management System"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07410 joss-papers#6184
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07410
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @Wytamma (Wytamma Wirth) and co-authors on your publication!!

And thanks to @huddlej and @beardymcjohnface for reviewing!
JOSS depends on volunteers and we couldn't do this without you

[editorialbot]

🎉🎉🎉 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.07410/status.svg)](https://doi.org/10.21105/joss.07410)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.07410/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07410/status.svg
   :target: https://doi.org/10.21105/joss.07410

This is how it will look in your documentation:

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[Wytamma]

Many thanks @danielskatz and to @huddlej and @beardymcjohnface. I know reviewing/editing takes a lot of time and I'm truely grateful for your contributions to this process. My work is far better off having had your inputs.