[REVIEW]: RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long sequences

[whedon]

Submitting author: @warrenlr (Rene L. Warren)
Repository: https://github.com/warrenlr/RAILS
Version: v1.1
Editor: @biorelated
Reviewer: @andrewjpage
Archive: https://dx.doi.org/10.5281/zenodo.167092

Status

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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 questions

Conflict of interest

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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: Does the release version given match the GitHub release (v1.1)?
• Authorship: Has the submitting author (@warrenlr) made major contributions to the software?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: Have any performance claims of the software been confirmed?

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)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS.

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

@whedon commands

[andrewjpage]

Good work @warrenlr and thanks for making all the changes I suggested.

[arfon]

Thanks for completing the review @andrewjpage. I've reopened the issue as I haven't finished all of the editorial tasks yet for this paper.

@warrenlr - one small suggestion - would you mind renaming the gpl-3.0.md file to LICENSE - this is a more 'standard' way to include a license file in a repository.

[warrenlr]

ok -- done

[arfon]

Thanks @warrenlr. At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[warrenlr]

Thank you @arfon for editing this submission.
The reviewed software is now archived in Zenodo, with DOI: 10.5281/zenodo.167092

Thanks,
Rene

[george-githinji]

Thank you @andrewjpage for reviewing the work. @arfon over to you for acceptance.

[arfon]

@biorelated - many thanks for editing this submission. @andrewjpage - thanks for the review!

@warrenlr - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00116 🎉 🚀 💥

[warrenlr]

This is great!
@arfon, @andrewjpage, @biorelated : many thanks for the swift review and the pleasant experience!

[vchuravy]

⚠️ An error happened when generating the pdf.