[PRE REVIEW]: TipToft: detecting plasmids contained in uncorrected long read sequencing data

[whedon]

Submitting author: @andrewjpage (Andrew Page)
Repository: https://github.com/andrewjpage/tiptoft
Version: v0.1.4
Editor: @Kevin-Mattheus-Moerman
Reviewers: @ctb, @kapsakcj, @azneto

Author instructions

Thanks for submitting your paper to JOSS @andrewjpage. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@andrewjpage if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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.

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1010 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: affiliations (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:69:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:99: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

'

[arfon]

@mgymrek - would you be willing to edit this submission for JOSS?

[arfon]

@andrewjpage - please take at look at the example paper in our submission requirements and format the YAML header of your paper the same way. Also, please note that YAML is white-space sensitive when making these changes.

Once you've made your changes you can ask @whedon to recompile your paper with the command @whedon generate pdf

[andrewjpage]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[andrewjpage]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[andrewjpage]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[andrewjpage]

I would like to propose the following reviewers:
@kapsakcj
@ctb
@azneto

[ctb]

happy to review but might take me three weeks...

[kapsakcj]

I'd also be happy to review. Thanks for nominating me to review @andrewjpage ! I will say though, that this would be my first time formally reviewing a manuscript and first time reviewing open-source software, so any advice or instructions would be welcomed. I have found the JOSS reviewer guidelines here to get me started. If you'd like to choose a more experienced reviewer, that would be fine with me.

[Kevin-Mattheus-Moerman]

@whedon assign @Kevin-Mattheus-Moerman as editor

[whedon]

OK, the editor is @Kevin-Mattheus-Moerman

[Kevin-Mattheus-Moerman]

@whedon assign @ctb as reviewer

[whedon]

OK, the reviewer is @ctb

[Kevin-Mattheus-Moerman]

@whedon add @kapsakcj as reviewer

[whedon]

OK, @kapsakcj is now a reviewer

[Kevin-Mattheus-Moerman]

@kapsakcj thanks for your comments. I am here to guide you all through the review process. Let me know if you have any questions. We will be recruiting multiple reviewers. I hope this first review experience will be a good one. Thanks! 🤖 🚀

[Kevin-Mattheus-Moerman]

@rozovr @fmaguire @azneto @mwhall @peterjc @tseemann would you be interested in reviewing this work for the Journal of Open Source Software (JOSS)? The review process focuses on the software and a short paper.
Let me know if you have questions.

[ctb]

(I've reviewed a few JOSS papers, and had a few reviewed; never seen more than one reviewer, much less three. Is this a new policy?)

[danielskatz]

We've frequently moved to two

[ctb]

(a third is being solicited for this 'un)

[danielskatz]

For me, the number depends on my expertise on the topic

[Kevin-Mattheus-Moerman]

@ctb I tend to aim for at least two reviewers. Since this submission is off topic for me I intend to recruit at least one more. I think, unless it delays the review process, the more the merrier.

[azneto]

I'd be happy to do it, though it's my first time reviewing a submission for JOSS. Feel free to choose a more experienced reviewer.

[Kevin-Mattheus-Moerman]

@whedon add @azneto as reviewer

[whedon]

OK, @azneto is now a reviewer

[Kevin-Mattheus-Moerman]

Thanks @azneto that is fine. prior experience with JOSS is not a requirement. I'm here to guide you through the process.

[Kevin-Mattheus-Moerman]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in #1021. Feel free to close this issue now!

[fmaguire]

@Kevin-Mattheus-Moerman Sorry about the slow reply, I've been away on holiday and only just got back. Looks like you are sorted for this one but I'd be happy to review other submission in future.