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

[editorialbot]

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Submitting author: @wytamma (Wytamma Wirth) Repository: https://github.com/Wytamma/snk Branch with paper.md (empty if default branch): Version: v0.30.1 Editor: @danielskatz Reviewers: @huddlej, @beardymcjohnface Archive: Pending

Status

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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

@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

[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:

@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]

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]

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

[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

• [x] 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

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

General checks

• [x] 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
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] 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?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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

• [x] 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

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

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/Wytamma/snk?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] 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?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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]

@Wytamma - It looks like there are a bunch of issues still open. I assume you are working on them. Can you provide an update of your status on them?

[Wytamma]

Hi @danielskatz I’ve been off sick but will try to get to all the remaining issues by the end of the week. -W

[Wytamma]

Hi @danielskatz - I've now address all the issues raised by my wonderful reviewers @huddlej and @beardymcjohnface! I did make a small change to the manuscript so it'll need to be rebuilt.

[danielskatz]

@editorialbot generate pdf

@Wytamma - you can run both of these commands too...

[danielskatz]

@editorialbot check references

[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]

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

[Wytamma]

Sorry I totally forgot! Thanks for the reminder :)

[huddlej]

@danielskatz I checked the final remaining box in my checklist, based on @Wytamma's responses to the issues linked above. Happy to see this published!

[danielskatz]

Thanks @huddlej

[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 https://github.com/Wytamma/snk/pull/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