[REVIEW]: LTRpred: de novo annotation of intact retrotransposons

whedon commented 4 years ago

Submitting author: @HajkD (Hajk-Georg Drost) Repository: https://github.com/HajkD/LTRpred Version: v1.1.0 Editor: @lpantano Reviewers: @dcassol, @mdozmorov Archive: 10.5281/zenodo.3895754

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/eeb2359d2459d3ae448cafac3ae33211/status.svg)](https://joss.theoj.org/papers/eeb2359d2459d3ae448cafac3ae33211)

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

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

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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 two weeks ✨

Review checklist for @dcassol

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 (@HajkD) 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 @mdozmorov

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 (@HajkD) 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 4 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/1497

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1497, 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 commented 4 years ago

@HajkD - looks like most of your references need a doi field added. Can you check the suggestions from Whedon above and if they are correct add them?

Also, just as a heads-up, these should be formatted without the https://doi.org/ bit, i.e. the BibTeX field should look like:

doi=10.1038/s41467-017-01374-x

HajkD commented 4 years ago

Dear @arfon

I now added doi fields to all references in the bib file and tested all the doi links. They are all correct and after checking with http://whedon.theoj.org it seems like the manuscript is in excellent shape.

Thank you very much for catching these issues!

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1093/nar/gkv1272 is OK
- 10.1093/nar/gkr367 is OK
- 10.7717/peerj.2584 is OK
- 10.1093/bioinformatics/btq461 is OK
- 10.1109/tcbb.2013.68 is OK
- 10.1093/nar/gkp759 is OK
- 10.1186/1471-2105-9-18 is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.1371/journal.pcbi.1003118 is OK
- 10.21105/joss.01686 is OK
- 10.1038/nrg.2016.139 is OK
- 10.1371/journal.pgen.1008370 is OK
- 10.1093/gbe/evz255 is OK
- 10.1038/s41477-018-0320-9 is OK
- 10.1093/bioinformatics/btw821 is OK
- 10.1038/s41467-020-14995-6 is OK
- 10.1186/gb-2012-13-8-r77 is OK
- 10.1038/s41467-017-01374-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 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/1498

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1498, 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 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 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/1499
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02170
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 4 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.02170/status.svg)](https://doi.org/10.21105/joss.02170)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02170">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02170/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02170/status.svg
   :target: https://doi.org/10.21105/joss.02170

This is how it will look in your documentation:

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HajkD commented 4 years ago

Dear all,

Thank you very much for all your efforts. As always it has been a pleasure submitting software to JOSS. Please keep up the excellent work and I very much look forward to collaborating with you on future projects.

With very best wishes, Hajk

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