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

[editorialbot]

Submitting author: !--author-handle-->@wytamma<!--end-author-handle-- (Wytamma Wirth) Repository: https://github.com/Wytamma/snk Branch with paper.md (empty if default branch): Version: v0.30.1 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @huddlej, @beardymcjohnface Managing EiC: Daniel S. Katz

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Author instructions

Thanks for submitting your paper to JOSS @wytamma. Currently, there isn't a JOSS editor assigned to your paper.

@wytamma if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1868.3 files/s, 139688.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        16            470              0           1167
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           2433
-------------------------------------------------------------------------------

Commit count by author:

   500  Wytamma Wirth
     6  Robert Turnbull
     1  Katherine Eaton

[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]

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:

[editorialbot]

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Acanthophis: a comprehensive plant hologenomics pipeline Submitting author: @kdm9 Handling editor: @marcosvital (Active) Reviewers: @bricoletc, @gbouras13, @abhishektiwari Similarity score: 0.6926

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

👋 @Wytamma - thanks for your submission. Due to the relatively small amount of code, the editors will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. You should hear back in a week or two.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Wytamma]

Thanks @danielskatz,

Just FYI the majority of the code is in the snk sister project Snk-CLI. There are two different projects so that users can use Snk-CLI without depending on the main Snk application. Details here -> https://snk.wytamma.com/workflow_packages and in the paper.md.

Kind regards,

Wytamma

[danielskatz]

Thanks @Wytamma

[danielskatz]

@Wytamma - this has passed the scope review, so we'll accept it for review. I'll assign myself as the editor

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[danielskatz]

Please suggest ~5 potential reviewers. You can search the list of people that have already agreed to review and may be suitable for this submission. Or people who aren't in the JOSS system would also be ok. If you know their GitHub usernames, then please mention them here in this thread (without tagging them with an @).

[Wytamma]

Thanks @danielskatz!

I've added potential reviewers here: beardymcjohnface, cmeesters, kdm9, huddlej & miparedes.

[danielskatz]

👋 @beardymcjohnface, @cmeesters, @kdm9 - would one or even two of you be willing to review this JOSS submission?

[danielskatz]

👋 @huddlej & @miparedes, would one or both of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[cmeesters]

Yes, but I have to admit, that the time I can spend on this is scarce until mid/end November. So it depends on your deadline. I do not want to be unfair to the author and take ages to review.

Given the length of that paper, I estimate that the time to review is dominated by testing. So my estimate would be end of November + 2-3 weeks (just before Christmas, I'm afraid).

[danielskatz]

@cmeesters - I think that will be ok, but let's see what other potential reviewers say. Thanks!

[kdm9]

I'm in the same position as @cmeesters: happy to, but likely to be slow.

[danielskatz]

thanks @kdm9 - I'll also wait and see about others in your case

[huddlej]

@danielskatz I'm available to review.

[danielskatz]

thanks @huddlej - I will add you now and see how we do on getting at least one more person before we start

[danielskatz]

@editorialbot add @huddlej as reviewer

[editorialbot]

@huddlej added to the reviewers list!

[beardymcjohnface]

This looks interesting, count me in :)

[danielskatz]

thanks @beardymcjohnface - I'll add you, and start the review

[danielskatz]

@editorialbot add @beardymcjohnface as reviewer

[editorialbot]

@beardymcjohnface added to the reviewers list!

[danielskatz]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7410.