[PRE REVIEW]: Dnaapler: A tool to reorient circular microbial genomes

[editorialbot]

Submitting author: @gbouras13 (George Bouras)
Repository: https://github.com/gbouras13/dnaapler
Branch with paper.md (empty if default branch):
Version: v0.2.0
Editor: @fboehm
Reviewers: @mkerin, @vinisalazar
Managing EiC: Kevin M. Moerman

Status

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Author instructions

Thanks for submitting your paper to JOSS @gbouras13. Currently, there isn't a JOSS editor assigned to your paper.

@gbouras13 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (677.2 files/s, 76313.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            440            388           1636
Markdown                        12            251              0            602
YAML                             7             25             10            155
TeX                              1             14              0            145
TOML                             1              7              0             38
Bourne Shell                     1              2              0              6
-------------------------------------------------------------------------------
SUM:                            33            739            398           2582
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/s13059-015-0849-0 is OK
- 10.1101/pdb.top17 is OK
- 10.1016/S0022-2836(05)80360-2 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1371/journal.pcbi.1005595 is OK
- 10.1093/nargab/lqab067 is OK
- 10.1186/s13059-021-02483-z is OK
- 10.1101/2023.04.04.535632 is OK
- 10.1093/bioinformatics/btad409 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 981

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[gbouras13]

Some people who would be good reviewers:

• Michael Hall https://reviewers.joss.theoj.org/reviewers/2619 - while he is in the acknowledgements as we copied & modified some of his code, this was done without any of his input & he has had nothing to do with Dnaapler.
• Curtis Kapsak https://reviewers.joss.theoj.org/reviewers/1647
• Justine Debelius https://reviewers.joss.theoj.org/reviewers/2113
• Vini Salazar https://reviewers.joss.theoj.org/reviewers/1974
• Andrea Telatin https://reviewers.joss.theoj.org/reviewers/1383

[Kevin-Mattheus-Moerman]

@gbouras13 thanks for this submission. I am the AEiC for this track and here to help with initial steps. Apologies for the delay so far. I have been out of the office for a while but am picking this up now.

Note I have just added the query-scope flag. This is to trigger a scope review by the editorial board. We usually do this for submissions that are rather small in size. The scope review will determine if this work is judged to conform to our substantial scholarly effort criteria. This review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

@gbouras13 I am pleased to inform you that this submission has passed the initial scope review. We'll now proceed to find a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @jmschrei as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@lucydot I think @jmschrei is actually not available. Do you think you can help with this one?

[Kevin-Mattheus-Moerman]

@editorialbot invite @lucydot as editor

[editorialbot]

Invitation to edit this submission sent!

[lucydot]

Hi @Kevin-Mattheus-Moerman I'm afraid this is a little too far outside of my area to feel comfortable editing.

[Kevin-Mattheus-Moerman]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[fboehm]

@editorialbot assign me as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

@Kevin-Mattheus-Moerman - thank you for the invitation! I'm happy to edit this submission.

[fboehm]

hi, @gbouras13 - my name is Fred, and I'm a JOSS editor. I'll work with you throughout the review of your submission.
The first step is for us to find two reviewers. Thank you so much for suggesting reviewers above. I'll contact them and others with similar expertise to ask about their interest and availability to review.
It's probably easiest for me if we communicate here (ie, in this github thread), although I'm happy to communicate about any sensitive matters via email.
Once we identify two reviewers, we'll "officially" start the review. Subsequent notifications and communications will then occur in another (not yet created) github thread. You should get notifications (ie, github "@" mentions for your username) when all of these events occur.
Please let me know if you have any questions. if not, then it should be a matter of a few days before we get the reviewers and start the review.
Thanks!

[fboehm]

@mkerin - would you like to review this submission?

[fboehm]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[fboehm]

@mbhall88 @kapsakcj @jwdebelius @vinisalazar @telatin - would you be willing to review this submission for JOSS? Thank you for considering this invitation.

[vinisalazar]

Hi @fboehm, thank you for the invite. I would be glad to review this.

[gbouras13]

Thanks for taking this on Fred @fboehm.

The only thing I will add is in the intervening period between me suggesting @telatin and now, I have e-met him and we are collaborating on an unrelated project. So probably it would be best if he is not a reviewer for this.

George

[mkerin]

Thank you for the invite @fboehm - I am also happy to review.

[fboehm]

Thank you, @gbouras13 for the updated information and transparency.

It looks like we've found two reviewers - I'll officially add them as reviewers in a moment. We can then start the reviews.

Thank you, @mkerin and @vinisalazar ! I'll add you as reviewers in a moment. Please follow the hyperlink that gets printed in the comment thread here to find the "review issue" for this submission. (PS - where we're now communicating is termed by JOSS as the "pre-review" thread). We'll communicate in the "review issue" / thread starting right away.

[fboehm]

@editorialbot add @mkerin as reviewer

[editorialbot]

@mkerin added to the reviewers list!

[fboehm]

@editorialbot add @vinisalazar as reviewer

[editorialbot]

@vinisalazar added to the reviewers list!

[fboehm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5968.