[REVIEW]: cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files

whedon commented 4 years ago

Submitting author: @lincoln-harris (Lincoln Harris) Repository: https://github.com/czbiohub/cerebra Version: v1.2.0 Editor: @lpantano Reviewer: @betteridiot, @afrubin Archive: 10.5281/zenodo.4050557

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Status

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Markdown: [![status](https://joss.theoj.org/papers/44041ee73f22ed846090242bdcda616a/status.svg)](https://joss.theoj.org/papers/44041ee73f22ed846090242bdcda616a)

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

@betteridiot & @afrubin, 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 try and complete your review in the next six weeks ✨

Review checklist for @betteridiot

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 (@lincoln-harris) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @afrubin

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 (@lincoln-harris) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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

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

- 10.1093/bioinformatics/btl647 is OK
- 10.1093/bioinformatics/btp324 is OK
- 10.1093/nar/gky1015 is OK
- 10.1016/j.cell.2017.09.004 is OK
- 10.1093/nar/gkz966 is OK
- 10.1038/s41587-019-0074-6 is OK
- 10.1038/nbt.2835 is OK
- 10.1101/201178 is OK
- 10.1002/humu.22981 is OK
- 10.1186/s13059-017-1248-5 is OK
- 10.1016/j.cell.2020.07.017 is OK
- 10.7287/peerj.preprints.970v1 is OK
- 10.1093/bioinformatics/bts635 is OK
- 10.21105/joss.00085 is OK

MISSING DOIs

- 10.25080/majora-ebaa42b7-00d may be a valid DOI for title: Building a framework for predictive science

INVALID DOIs

- arXiv:1207.3907v2 is INVALID

whedon commented 3 years ago

PDF failed to compile for issue #2432 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:77:in doi_citation': undefined methodencode' for nil:NilClass (NoMethodError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:64:in make_citation' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:50:inblock in generate_citations' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:43:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/compilers.rb:246:incrossref_from_markdown' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/processor.rb:95:incompile' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:82:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' 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:indispatch' 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-364ded062842/bin/whedon:119: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

'

Kevin-Mattheus-Moerman commented 3 years ago

@lincoln-harris I am helping to process the acceptance of this work in JOSS. Can you work on the points below?

[x] You have one invalid DOI :point_up:, this is because you link to an arXiv preprint link rather than a valid DOI. Can you change the doi entry in the bib file to be of the url type instead? I believe this involves replacing:
```
doi={arXiv:1207.3907v2}
```
with
```
url={https://arxiv.org/abs/1207.3907}
```
[x] Please add a country to your affiliation(s) (please do not use acronyms for countries)
[x] The hyperlink to ENSEMBL in Protein variants are converted to ENSEMBL protein IDs,..., appears not to work, please check and update.

Kevin-Mattheus-Moerman commented 3 years ago

@openjournals/dev I identified the invalid DOI but am unsure if this is the reason the paper does not compile for @whedon accept, can you confirm what the issue is here? Thanks

lincoln-harris commented 3 years ago

@Kevin-Mattheus-Moerman done, hopefully that takes care of it.

Kevin-Mattheus-Moerman commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

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/1770

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1770, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman 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/1771
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02432
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

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.02432/status.svg)](https://doi.org/10.21105/joss.02432)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02432">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02432/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02432/status.svg
   :target: https://doi.org/10.21105/joss.02432

This is how it will look in your documentation:

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Kevin-Mattheus-Moerman commented 3 years ago

Congratulations @lincoln-harris!

Thanks for your review efforts @betteridiot, @afrubin, also thank you @lpantano for editing!

lincoln-harris commented 3 years ago

awesome!! thanks @betteridiot, @afrubin and @lpantano!! I learned a ton through the review process

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