[PRE REVIEW]: CPgeneProfiler: A lightweight R package to profile the Carbapenamase genes from genome assemblies

[whedon]

Submitting author: @ramadatta (Prakki Sai Rama Sridatta)
Repository: https://github.com/ramadatta/CPgeneProfiler
Version: v2.1.0
Editor: @will-rowe
Reviewers: @fmaguire, @boasvdp
Managing EiC: Kyle Niemeyer

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

@ramadatta 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 @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2453 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2453 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
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:in dispatch'
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-446a0298a33b/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

'

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1093/bioinformatics/btx364 may be missing for title: UpSetR: an R package for the visualization of intersecting sets and their properties
- https://doi.org/10.1186/1471-2105-10-421 may be missing for title: BLAST+: architecture and applications
- https://doi.org/10.1186/s13073-014-0090-6 may be missing for title: SRST2: rapid genomic surveillance for public health and hospital microbiology labs
- https://doi.org/10.1093/jac/dks261 may be missing for title: Identification of acquired antimicrobial resistance genes
- https://doi.org/10.1093/nar/gkw1009 may be missing for title: MEGARes: an antimicrobial resistance database for high throughput sequencing
- https://doi.org/10.1093/nar/gkw1004 may be missing for title: CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
- https://doi.org/10.1128/aac.01310-13 may be missing for title: ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
- https://doi.org/10.1099/mgen.0.000131 may be missing for title: ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
- https://doi.org/10.3389/fpubh.2019.00242 may be missing for title: Using genomics to track global antimicrobial resistance
- https://doi.org/10.1093/ofid/ofx176 may be missing for title: Prevalence of carbapenem-resistant Gram-negative infections in the United States predominated by Acinetobacter baumannii and Pseudomonas aeruginosa
- https://doi.org/10.1016/j.jinf.2018.11.003 may be missing for title: Whole genome sequencing detects inter-facility transmission of carbapenem-resistant Klebsiella pneumoniae
- https://doi.org/10.1128/aac.02282-18 may be missing for title: Cocarriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single sequence type 11 carbapenem-resistant Klebsiella pneumoniae isolate
- https://doi.org/10.1093/cid/ciz824 may be missing for title: Epidemiology and diagnostics of carbapenem resistance in gram-negative bacteria

INVALID DOIs

- None

[kyleniemeyer]

Hi @ramadatta, thanks for your submission. It looks like there is a problem with your paper.md file. As a start, can you try removing these fields from the header?

citation_author: Prakki et. al.
year: 2020
output: rticles::joss_article
csl: apa.csl
journal: JOSS

(just leave the bibliography field in that section of lines, and date is ok too)

As you edit this, you can use this page to test that the paper builds properly: https://whedon.theoj.org

[kyleniemeyer]

Hi @will-rowe, could you edit this submission?

[kyleniemeyer]

@whedon invite @will-rowe as editor

[whedon]

@will-rowe has been invited to edit this submission.

[arfon]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[ramadatta]

Hi @ramadatta, thanks for your submission. It looks like there is a problem with your paper.md file. As a start, can you try removing these fields from the header?

citation_author: Prakki et. al.
year: 2020
output: rticles::joss_article
csl: apa.csl
journal: JOSS

(just leave the bibliography field in that section of lines, and date is ok too)

As you edit this, you can use this page to test that the paper builds properly: https://whedon.theoj.org

Dear @kyleniemeyer, thank you very much! I have edited paper.md according to your advice. The modified paper.md builds properly with the Whedon paper preview service.

[will-rowe]

@whedon assign @will-rowe as editor

[whedon]

OK, the editor is @will-rowe

[will-rowe]

Hi @flashton2003, @fmaguire, @alexwailan. Do you have time to review this for JOSS?

[fmaguire]

@will-rowe sure, I'd be more than happy to review this submission.

[will-rowe]

Great - thanks @fmaguire! Let me find one more reviewer and then we'll kick of the review thread.

[will-rowe]

Hi @boasvdp - would you be able to review this submission please?

[boasvdp]

@will-rowe Sure thing! Count me in

[will-rowe]

Thanks folks! We'll start the review process now. Let me know if you need anything.

[will-rowe]

@whedon assign @fmaguire as reviewer

[whedon]

OK, @fmaguire is now a reviewer

[will-rowe]

@whedon add @boasvdp as reviewer

[whedon]

OK, @boasvdp is now a reviewer

[will-rowe]

@whedon start review

[whedon]

OK, I've started the review over in #2473.