[REVIEW]: nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline

[whedon]

Submitting author: @ZeyuanSong (Zeyuan Song)
Repository: https://github.com/montilab/nf-gwas-pipeline
Version: v1.0.0
Editor: @lpantano
Reviewers: @preetida, @rspirgel
Archive: 10.5281/zenodo.4565942

⚠️ 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.

Status

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Markdown: [![status](https://joss.theoj.org/papers/f83bc12a260f44a6166d3a4b71e3ed5e/status.svg)](https://joss.theoj.org/papers/f83bc12a260f44a6166d3a4b71e3ed5e)

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

@preetida,@rspirgel please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano 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 ✨

Review checklist for @rspirgel

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 (@ZeyuanSong) 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 @preetida

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 (@ZeyuanSong) 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. @preetida 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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1038/s41576-019-0127-1 is OK
- 10.1186/s12859-019-2964-5 is OK
- 10.1038/nbt.3820 is OK
- 10.1093/bioinformatics/btx145 is OK
- 10.1002/gepi.21896 is OK
- 10.1016/j.ajhg.2015.11.022 is OK
- 10.1093/bioinformatics/btz567 is OK
- 10.1016/j.ajhg.2016.02.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[lpantano]

@whedon add @rspirgel as reviewer

[whedon]

OK, @rspirgel is now a reviewer

[whedon]

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

[preetida]

Hi @lpantano,
I must have missed the checklist part.
It wouldn't allow me now and says the invitation expired.
Can you pls resend it.
Also, this is my first time reviewing for this journal,
for the issue with the tool, just open a new issue on their GitHub or report it here?
Thanks,
Preeti

[lpantano]

@whedon add @preetida as reviewer

[whedon]

OK, @preetida is now a reviewer

[lpantano]

Thank @preetida, I would use this for general discussion, and create an issue in their GitHub and mentioned here so we see what is going on. Let me know if you get the new invitation after trying to add you as reviewer again. Thanks!

[danielskatz]

@lpantano the better command to use in this instance is 👇

[danielskatz]

@whedon re-invite @preetida as reviewer

[whedon]

@preetida already has access.

[preetida]

@lpantano thank you, that worked this time.

[lpantano]

@preetida, can you check if the latest addition is enough? I just saw the authors closed the issue, so I don't know if there is something else waiting to be done? Thanks!

[whedon]

OK. 10.5281/zenodo.4565942 is the archive.

[lpantano]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41576-019-0127-1 is OK
- 10.1186/s12859-019-2964-5 is OK
- 10.1038/nbt.3820 is OK
- 10.1093/bioinformatics/btx145 is OK
- 10.1002/gepi.21896 is OK
- 10.1016/j.ajhg.2015.11.022 is OK
- 10.1093/bioinformatics/btz567 is OK
- 10.1016/j.ajhg.2016.02.012 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#2125

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2125, 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]

@ZeyuanSong or @anfederico - I'm suggesting two paper changes in montilab/nf-gwas-pipeline#3, to make the list work (hopefully) and to remove an extra work. Please merge this and see if it fixes the list (by running @whedon generate pdf) or let me know what you disagree with

[ZeyuanSong]

@whedon generate pdf

[whedon]

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

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41576-019-0127-1 is OK
- 10.1186/s12859-019-2964-5 is OK
- 10.1038/nbt.3820 is OK
- 10.1093/bioinformatics/btx145 is OK
- 10.1002/gepi.21896 is OK
- 10.1016/j.ajhg.2015.11.022 is OK
- 10.1093/bioinformatics/btz567 is OK
- 10.1016/j.ajhg.2016.02.012 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#2126

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2126, 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.02957 joss-papers#2127
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02957
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 @ZeyuanSong (Zeyuan Song) and coauthors!!

And thanks to @preetida and @rspirgel for reviewing, and @lpantano for editing!

[whedon]

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

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reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02957/status.svg
   :target: https://doi.org/10.21105/joss.02957

This is how it will look in your documentation:

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[ZeyuanSong]

@danielskatz I forgot to add fundings in the paper, and I just added the fundings in the paper in Github. Could you help update the paper on the journal? Thanks!

[danielskatz]

I can't, but I think @arfon can update the paper manually...

[ZeyuanSong]

@arfon Sorry for the inconvenience caused by my mistake. Could you help edit the paper on the journal?

The updated paper is at [https://github.com/montilab/nf-gwas-pipeline/blob/master/paper/paper.md]. Or you can just substitute the Acknowledgements to "We thank for Harold Bae and Aparna Bhutkar for their help. This work was supported with funding from NIH/NIA: U19AG023122 (Longevity Consortium), and UH2AG064704 (Omics Profiles in Centenarians)."

Many thanks!

[arfon]

OK, that should be updated now. It may take a few hours for the version on the JOSS site to show as updated due to caching we have in place.