Joss-reviews: [REVIEW]: Kindel: indel-aware consensus for nucleotide sequence alignments

[whedon]

Submitting author: @bede (Bede Constantinides)
Repository: https://github.com/bede/kindel
Version: v0.2.0
Editor: @mgymrek
Reviewer: @genomematt
Archive: 10.5281/zenodo.826723

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/117efd1fc35bb2011311f73d3fa0b545/status.svg)](http://joss.theoj.org/papers/117efd1fc35bb2011311f73d3fa0b545)

Reviewers and authors:

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Reviewer questions

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v0.2.0)?
• [x] Authorship: Has the submitting author (@bede) made major contributions to the software?

Functionality

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

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @genomematt it looks like you're currently assigned as the reviewer for this paper :tada:.

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[genomematt]

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[whedon]

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[genomematt]

Looks quite good. Only issues are:
The lack of a clear example usage. I would recommend something that shows some input and output. (Probably easiest to do by just working through an analysis in an ipynb)

The paper is quite sparse. It definitely needs to cite ococo like the main page does. A simplified diagram example of input and output would help a lot, especially for someone slightly off field.

There are guidelines for reporting bugs and support, but no guidelines for contributing. See other JOSS articles for examples.

[bede]

Thanks for your comments Matt. I'll reply again once I've incorporated the following:

• Example usage (Jupyter notebook or otherwise)
• Additional detail to the paper, perhaps including a diagrammatic explanation of usage
• Contribution guidelines

[bede]

I've done the following:

• Created an example usage notebook
• Added detail to the paper, including two diagrams
• Reviewed a handful of accepted JOSS papers to see how they approached contribution guidelines, and added a section to the README

Are you happy with the changes @genomematt ?

[genomematt]

This now ticks all the boxes. I think we are ready to accept @mgymrek

[gymreklab]

This looks great to me. @arfon I think this is ready to go.

[arfon]

@bede - Could you move the references you currently have in the paper.md file into a paper.bib file and cite them directly please? (You can read how to do that here)

[bede]

@arfon Thanks! Now sorted.

I'd seen a lot of JOSS submissions using hardcoded citations and just followed suit. This is much cleaner.

[bede]

@arfon Also, is it possible to revise the text on this page? http://joss.theoj.org/papers/117efd1fc35bb2011311f73d3fa0b545

[arfon]

@arfon Also, is it possible to revise the text on this page?

This will be replaced by your paper content once we've accepted the paper.

Thanks for making the edits to paper.md, take a look at the compiled PDF here 10.21105.joss.00282.pdf

I'm wondering if you should remove the sections (Core functionality etc) and just replace these with slightly longer captions? The flow of the document in Pandoc is pretty weird. Smaller figures might help too.

[bede]

@arfon Thanks for your comments. I (think I) now understand how Rmd citations and figure captions work. Things should look better next time you compile.

[arfon]

@arfon Thanks for your comments. I (think I) now understand how Rmd citations and figure captions work. Things should look better next time you compile.

That's looking good. Thanks. At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[bede]

Thanks – here it is: https://doi.org/10.5281/zenodo.826723

[arfon]

@whedon set 10.5281/zenodo.826723 as archive

[whedon]

OK. 10.5281/zenodo.826723 is the archive.

[arfon]

@genomematt - many thanks for your review here and to @mgymrek for editing this submission ✨

@bede - your paper is now accepted into JOSS. Your DOI is http://dx.doi.org/10.21105/joss.00282 ⚡️ 🚀 💥

[bede]

Arfon, Matt and Melissa, thank you all for your time.