[PRE REVIEW]: Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance

[editorialbot]

Submitting author: @jhayer (Juliette Hayer)
Repository: https://github.com/jhayer/baargin
Branch with paper.md (empty if default branch):
Version: v0.1
Editor: @fboehm
Reviewers: @mberacochea, @rcannood
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2"><img src="https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2/status.svg)](https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2)

Author instructions

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

@jhayer if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (140.7 files/s, 20766.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            180            230            797
Markdown                         2            114              0            385
TeX                              1             16              0            292
YAML                             3              5              9             39
-------------------------------------------------------------------------------
SUM:                            14            315            239           1513
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1231

[editorialbot]

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

OK DOIs

- 10.1038/D41586-022-00228-X is OK
- 10.1038/nbt.3820 is OK
- 10.1093/BIOINFORMATICS/BTY560 is OK
- 10.1002/CPBI.102 is OK
- 10.1371/JOURNAL.PCBI.1005595 is OK
- 10.1038/S41596-022-00738-Y is OK
- 10.1093/BIOINFORMATICS/BTT086 is OK
- 10.1093/MOLBEV/MSAB199 is OK
- 10.1128/AAC.02412-14 is OK
- 10.1099/MGEN.0.000398 is OK
- 10.1093/NAR/GKAC920 is OK
- 10.1038/s41598-021-91456-0 is OK
- 10.1093/BIOINFORMATICS/BTU153 is OK
- 10.1099/MGEN.0.000685 is OK
- 10.1093/BIOINFORMATICS/BTV421 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1186/S13059-019-1891-0/FIGURES/2 is INVALID

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@jhayer I am the AEiC for this track and here to process initial steps. I have just flagged this submission for a scope review by our editorial board. This is normal for submissions of this size. The scope review should be completed within about 2 weeks and will determined if this submission conforms to our substantial scholarly effort criteria.

[Kevin-Mattheus-Moerman]

@jhayer I am pleased to report this work has passed our initial scope check. We will now proceed to recruit a handling editor. Note that during review the scope may be queried again.

[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 to edit this submission. I'm happy to do so.

[Kevin-Mattheus-Moerman]

@editorialbot assign @fboehm as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

@jhayer - I'll be editing your submission. Can you suggest individuals who might serve as reviewers? We'll need to recruit two reviewers. They don't need to be individuals who have reviewed for JOSS in the past. Thank you!

[fboehm]

@editorialbot list reviewers

[editorialbot]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[fboehm]

@jhayer - you can look at the link above to help in choosing reviewers. I'm also happy to invite individuals who are not on that list. Ideally, reviewers would have expertise in your area of research.

[jhayer]

@fboehm - I can suggest the following reviewers from the JOSS list:

• coughls
• mberacochea
• rcannood

Please let me know if you need additional suggestions.

[fboehm]

Thank you, @jhayer ! I'll reach out to the suggested reviewers now.

[fboehm]

@coughls @mberacochea @rcannood - Would you like to review this submission to JOSS? Our reviews are checklist-driven, meaning that we provide you with a checklist and you verify that the submission meets each of the specified criteria. Please let me know if you're available to review. Thank you!

[mberacochea]

@coughls @mberacochea @rcannood - Would you like to review this submission to JOSS? Our reviews are checklist-driven, meaning that we provide you with a checklist and you verify that the submission meets each of the specified criteria. Please let me know if you're available to review. Thank you!

I'm happy to review this one 👍

[rpetit3]

👋 Am I no longer needed for this?

[fboehm]

wave Am I no longer needed for this?

Sorry for the confusion, @rpetit3. You're no longer needed for this submission. I hope that we can work together on a future submission.

[fboehm]

@mberacochea - Thanks so much! I'll add you as a reviewer now. Once we have two reviewers, we'll proceed with the review.

[fboehm]

@editorialbot add @mberacochea as reviewer

[editorialbot]

@mberacochea added to the reviewers list!

[fboehm]

@jhayer - We need to find one more reviewer. Do you have any suggestions for additional reviewers? Please feel free to list their github handles (without a preceding "at" sign) in this thread.

[rcannood]

Happy to be reviewer number two :) 👋

[fboehm]

Thanks, @rcannood ! I'll add you now.

[fboehm]

@editorialbot add @rcannood as reviewer

[editorialbot]

@rcannood added to the reviewers list!

[fboehm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5397.