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

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f83bc12a260f44a6166d3a4b71e3ed5e"><img src="https://joss.theoj.org/papers/f83bc12a260f44a6166d3a4b71e3ed5e/status.svg"></a>
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:

Make sure you're logged in to your GitHub account
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

[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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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

Review checklist for @preetida

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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

whedon commented 3 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

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

watching

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

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 commented 3 years ago

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 commented 3 years ago

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

lpantano commented 3 years ago

@whedon add @rspirgel as reviewer

whedon commented 3 years ago

OK, @rspirgel is now a reviewer

whedon commented 3 years ago

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

preetida commented 3 years ago

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 commented 3 years ago

@whedon add @preetida as reviewer

whedon commented 3 years ago

OK, @preetida is now a reviewer

lpantano commented 3 years ago

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 commented 3 years ago

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

danielskatz commented 3 years ago

@whedon re-invite @preetida as reviewer

whedon commented 3 years ago

@preetida already has access.

preetida commented 3 years ago

@lpantano thank you, that worked this time.

lpantano commented 3 years ago

@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!

preetida commented 3 years ago

@lpantano Yes, the guidelines have been added to the paper. Looks all set.

lpantano commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

lpantano commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

lpantano commented 3 years ago

@ZeyuanSong , 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 accepting the submission.

anfederico commented 3 years ago

[x] Make a tagged release of your software, and list the version tag of the archived version here.

v.1.00 (Publication Release) tagged on Github https://github.com/montilab/nf-gwas-pipeline/releases/tag/v1.00

[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

[x] 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.

Archived: https://zenodo.org/record/4565942#.YDkzxy2ZNE4

[x] Please list the DOI of the archived version here.

lpantano commented 3 years ago

@whedon set 10.5281/zenodo.4565942 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4565942 is the archive.

lpantano commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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 commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2125

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

@ZeyuanSong or @anfederico - I'm suggesting two paper changes in https://github.com/montilab/nf-gwas-pipeline/pull/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 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

danielskatz commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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 commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2126

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2127
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02957
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

Congratulations to @ZeyuanSong (Zeyuan Song) and coauthors!!

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

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02957/status.svg)](https://doi.org/10.21105/joss.02957)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02957">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02957/status.svg" alt="DOI badge" >
</a>

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:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

ZeyuanSong commented 3 years ago

@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 commented 3 years ago

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

ZeyuanSong commented 3 years ago

@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 commented 3 years ago

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.

openjournals / joss-reviews