[REVIEW]: Nanoq: fast quality control for nanopore reads

[whedon]

Submitting author: @esteinig (Eike J. Steinig)
Repository: https://github.com/esteinig/nanoq
Version: v0.8.3
Editor: @luizirber
Reviewer: @natir, @bovee
Archive: 10.5281/zenodo.5816183

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Review checklist for @natir

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 repository url?
• 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 (@esteinig) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @bovee

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 repository url?
• 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 (@esteinig) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @natir, @bovee it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btv573 is OK
- 10.1016/S1473-3099(20)30562-4 is OK
- 10.1093/bioinformatics/bty149 is OK
- 10.1038/nbt.4060 is OK
- 10.1093/gigascience/giz043 is OK
- 10.1093/bioinformatics/bty654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

👋 @natir, please update us on how your review is going.

[whedon]

👋 @bovee, please update us on how your review is going.

[esteinig]

@natir @bovee still working on the improvements, apologies for the delay

[luizirber]

We are in the middle of a pandemic, so whedon's comment might sound a bit demanding, but the intentions are good, just so we know how the review is going =]

@esteinig do you mind opening a PR with the joss branch, so we have better visibility on the changes you're making to address Roderick and Pierre's comments? You don't need to merge the PR yet, but it is nicer to see changes than having to find the branch in the nanoq repo.

[esteinig]

@luizirber thanks a ton, really appreciate the patience! I am back on this from tomorrow, so will make the PR request and finalize all the bits and pieces (not sure if you want to see my messy commit history but all good). Thanks everyone!

[esteinig]

@luizirber my sincere apologies for the delays. I'm in the process of submitting my PhD thesis and it's a bit hectic. I hope this is not an issue. I would very much like to include the (excellent) points raised by the reviewers and include documentation and other improvements.

[luizirber]

@esteinig I don't see any problems in delaying a bit, thesis work is hard. Good luck!

Just checking with @openjournals/joss-eics if there is any specific whedon command or tag to be added to show that this submission is paused, or just leave as-is.

[arfon]

Just checking with @openjournals/joss-eics if there is any specific whedon command or tag to be added to show that this submission is paused, or just leave as-is.

We just add the paused label in situations like this. I'll add it now...

[arfon]

👋 folks, just checking in here. @esteinig - did you manage to submit your thesis yet?

[arfon]

👋 @esteinig – any updates here?

[natir]

@whedon generate pdf

[whedon]

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

[luizirber]

Removing the paused label, let's get this going again? =]

[whedon]

OK. v0.8.3 is the version.

[luizirber]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btv573 is OK
- 10.1371/journal.pone.0163962 is OK
- 10.1016/S1473-3099(20)30562-4 is OK
- 10.1093/bioinformatics/bty149 is OK
- 10.1038/nbt.4060 is OK
- 10.1093/gigascience/giz043 is OK
- 10.1093/bioinformatics/bty654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2766

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2766, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[esteinig]

Wohooo, looking good! 🥳 Thanks so much for your patience and feedback, really appreciated this process.

[Kevin-Mattheus-Moerman]

@luizirber thanks for editing this work. Some points need to be addressed here which you can keep in mind for the future so you fix these before recommending acceptance. In particular the archived version meta-data (title, author lists, etc) should match that of the paper.

[Kevin-Mattheus-Moerman]

@esteinig I have reviewed your paper and the archived data and have the following issues that need your attention:

• Edit the ZENODO archive such that the meta-data matches the paper (you can do this manually).

• The title should be: Nanoq: ultra-fast quality control for nanopore reads.

• The author lists should match the paper

• You may also add ORCID profiles to the authors on ZENODO

• Check throughout for potentially missing "Oxford comma's" E.g. perhaps here? Nanoq offers nanopore-specific quality scores, read filtering options[,] and output compression.

• Check ...they may not immediately applicable..., looks like that should be ...they may not be immediately applicable...?

• Check ...and summary statistics on the even.... It may be because this is not my domain of expertise but this sentence does not make sense to me. It is mainly the "on the even" part that throws me off. Consider rephrasing.

• If it is easy to recreate figures 1 and 2 I suggest/recommend (not required) to render them with a larger font size and to export them with a higher resolution.

[Kevin-Mattheus-Moerman]

@esteinig could you give an update on work on this ☝️. Let us know if you have any questions.

[esteinig]

@Kevin-Mattheus-Moerman thanks so much for the final suggestions, will upload the new version over the weekend! (apologies for the delay)

[arfon]

@esteinig – just checking if you've managed to make these changes yet?

[esteinig]

@arfon yes thanks so much for your patience, the end of last year was a bit hectic for us. please see the new version pushed:

• Zenodo data updated
• oxford commas added throughout manuscript
• spelling checked and fixed

thank you to all of the editors and reviewers involved with this! my apologies it took me so long (we have been involved with the pandemic here in australia) really do appreciate all your patience 🙏

[danielskatz]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btv573 is OK
- 10.1371/journal.pone.0163962 is OK
- 10.1016/S1473-3099(20)30562-4 is OK
- 10.1093/bioinformatics/bty149 is OK
- 10.1038/nbt.4060 is OK
- 10.1093/gigascience/giz043 is OK
- 10.1093/bioinformatics/bty654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon set 10.5281/zenodo.5816183 as archive

[whedon]

OK. 10.5281/zenodo.5816183 is the archive.

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2870

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2870, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.02991 joss-papers#2871
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02991
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 @esteinig (Eike J. Steinig) and co-author!!

And thanks to @natir and @bovee for reviewing, and @luizirber for editing!
We couldn't do this without you!

[whedon]

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

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