[REVIEW]: WGS2NCBI - Toolkit for preparing genomes for submission to NCBI #1364

whedon · 2019-04-04T20:15:12Z

Submitting author: @rvosa (Rutger Vos)
Repository: https://github.com/naturalis/wgs2ncbi
Version: v1.0.3
Editor: @lpantano
Reviewer: @druvus
Archive: 10.5281/zenodo.2645762

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/72b726934646d999001e9997ad2fdb54"><img src="http://joss.theoj.org/papers/72b726934646d999001e9997ad2fdb54/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/72b726934646d999001e9997ad2fdb54/status.svg)](http://joss.theoj.org/papers/72b726934646d999001e9997ad2fdb54)

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) 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

@druvus, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @lpantano know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @druvus

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
Version: v1.0.3
Authorship: Has the submitting author (@rvosa) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

The text was updated successfully, but these errors were encountered:

whedon · 2019-04-04T20:15:15Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @druvus it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ 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:

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@whedon commands

whedon · 2019-04-04T20:15:17Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-04T20:15:40Z

👉 Check article proof 📄 👈

druvus · 2019-04-11T12:37:34Z

@rvosa I started to add issues to the wgs2ncbi repo regarding failing automatic tests, stalled help command and contribution documentation. Could you please take a look at them?

rvosa · 2019-04-11T14:17:07Z

on it, as I hope you can see :)

…

On Thu, Apr 11, 2019 at 2:37 PM Andreas Sjödin ***@***.***> wrote: @rvosa <https://github.com/rvosa> I started to add issues to the wgs2ncbi repo regarding failing automatic tests, stalled help command and contribution documentation. Could you please take a look at them? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1364 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAGf-hu1y8_8oYyz27ybA86Z73B6Az5Kks5vfyyQgaJpZM4cdn3W> .

druvus · 2019-04-17T19:36:55Z

thanks @rvosa ! I guess you should release an updated tagged version and update the manuscript to point to this new improved version.

druvus · 2019-04-17T19:39:43Z

@lpantano I happy with wgs2ncbi once the article is updated to include a new updated version based on latest wgs2ncbi commit.

rvosa · 2019-04-17T19:58:18Z

I tagged the most recent commit as v1.0.1 but I forgot where I need to insert that tag in the submission?

lpantano · 2019-04-17T20:39:10Z

@whedon set v1.0.1 as version

whedon · 2019-04-17T20:39:14Z

OK. v1.0.1 is the version.

lpantano · 2019-04-17T20:41:24Z

@whedon generate pdf

whedon · 2019-04-17T20:41:27Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-17T20:41:51Z

👉 Check article proof 📄 👈

lpantano · 2019-04-17T20:57:01Z

@whedon check references

whedon · 2019-04-17T20:57:04Z

Attempting to check references...

whedon · 2019-04-17T20:57:06Z


OK DOIs

- 10.1093/bib/bbv104 is OK
- 10.1093/nar/gku1216 is OK
- 10.1073/pnas.1314702110 is OK

MISSING DOIs

- None

INVALID DOIs

- None

lpantano · 2019-04-18T11:54:12Z

Thanks @druvus for the review!

@rvosa, can you create a Zenodo archive of your repository and give me the DOI? The title needs to match the papers title and make sure authors are correct in Zenodo as well.

Thanks!

rvosa · 2019-04-18T13:02:47Z

@rvosa <https://github.com/rvosa>, can you create a Zenodo archive of your repository and give me the DOI? The title needs to match the papers title and make sure authors are correct in Zenodo as well.

Tagged release v1.0.3 is now mirrored on Zenodo, with the same title as the manuscript, and with the coauthors embedded in the .zenodo.json file. The DOI for this release is 10.5281/zenodo.2645762

…

rvosa · 2019-04-18T13:15:37Z

@whedon generate pdf

whedon · 2019-04-18T13:15:40Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-18T13:16:12Z

👉 Check article proof 📄 👈

lpantano · 2019-04-19T20:57:15Z

@whedon set v1.0.3 as version

whedon · 2019-04-19T20:57:19Z

OK. v1.0.3 is the version.

lpantano · 2019-04-19T20:58:15Z

@whedon set 10.5281/zenodo.2645762 as archive

whedon · 2019-04-19T20:58:19Z

OK. 10.5281/zenodo.2645762 is the archive.

lpantano · 2019-04-19T20:59:14Z

Ok, @openjournals/joss-eics I think we are done. Please let me know if something is off.

arfon · 2019-04-19T23:32:40Z

@whedon accept

whedon · 2019-04-19T23:32:43Z

Attempting dry run of processing paper acceptance...

whedon · 2019-04-19T23:32:52Z

PDF failed to compile for issue #1364 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1364 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:73:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

whedon · 2019-04-19T23:33:28Z


OK DOIs

- 10.1093/bib/bbv104 is OK
- 10.1093/nar/gku1216 is OK
- 10.1073/pnas.1314702110 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon · 2019-04-19T23:33:32Z

@whedon accept

whedon · 2019-04-19T23:33:34Z

Attempting dry run of processing paper acceptance...

whedon · 2019-04-19T23:33:37Z


OK DOIs

- 10.1093/bib/bbv104 is OK
- 10.1093/nar/gku1216 is OK
- 10.1073/pnas.1314702110 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2019-04-19T23:34:00Z

Check final proof 👉 openjournals/joss-papers#633

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#633, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon · 2019-04-19T23:34:49Z

@whedon accept deposit=true

whedon · 2019-04-19T23:34:52Z

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

whedon · 2019-04-19T23:35:39Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.01364 joss-papers#634
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01364
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon · 2019-04-19T23:39:03Z

@druvus - many thanks for your review and to @lpantano for editing this one ✨

@rvosa - your paper is now accepted into JOSS ⚡️🚀💥

whedon · 2019-04-19T23:39:06Z

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

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whedon assigned lpantano Apr 4, 2019

whedon added the review label Apr 4, 2019

whedon mentioned this issue Apr 4, 2019

[PRE REVIEW]: WGS2NCBI - Toolkit for preparing genomes for submission to NCBI #1353

Closed

lpantano added the accepted label Apr 18, 2019

arfon closed this as completed Apr 19, 2019

lpantano mentioned this issue May 3, 2019

[REVIEW]: CRED: a rapid peak caller for Chem-seq data #1423

Closed

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whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

editorialbot mentioned this issue Oct 15, 2023

[PRE REVIEW]: 'cstag and cstag-cli: tools for manipulating and visualizing CS tags' #5950

Closed

[REVIEW]: WGS2NCBI - Toolkit for preparing genomes for submission to NCBI #1364

[REVIEW]: WGS2NCBI - Toolkit for preparing genomes for submission to NCBI #1364

Comments

whedon commented Apr 4, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @druvus

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Apr 4, 2019

whedon commented Apr 4, 2019

whedon commented Apr 4, 2019

druvus commented Apr 11, 2019

rvosa commented Apr 11, 2019 via email

druvus commented Apr 17, 2019

druvus commented Apr 17, 2019

rvosa commented Apr 17, 2019

lpantano commented Apr 17, 2019

whedon commented Apr 17, 2019

lpantano commented Apr 17, 2019

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lpantano commented Apr 17, 2019

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lpantano commented Apr 18, 2019

rvosa commented Apr 18, 2019 via email

rvosa commented Apr 18, 2019

whedon commented Apr 18, 2019

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lpantano commented Apr 19, 2019

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lpantano commented Apr 19, 2019

whedon commented Apr 19, 2019

lpantano commented Apr 19, 2019

arfon commented Apr 19, 2019

whedon commented Apr 19, 2019

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arfon commented Apr 19, 2019

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whedon commented Apr 4, 2019 •

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