[PRE REVIEW]: 'cstag and cstag-cli: tools for manipulating and visualizing CS tags'

[editorialbot]

Submitting author: @akikuno (Akihiro Kuno)
Repository: https://github.com/akikuno/cstag
Branch with paper.md (empty if default branch): joss
Version: v1.0.4
Editor: @jmschrei
Reviewers: @betteridiot, @jbloom
Managing EiC: Kevin M. Moerman

Status

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Author instructions

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

@akikuno 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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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1223.0 files/s, 107887.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24            442            428           1420
Markdown                         5            126              0            311
HTML                             4             51              0            288
TeX                              1             11              0            127
TOML                             1              2              0             23
YAML                             1              1              4             18
Bourne Shell                     1              3              4              5
-------------------------------------------------------------------------------
SUM:                            37            636            436           2192
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 792

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1093/bioinformatics/bty191 may be a valid DOI for title: Minimap2: pairwise alignment for nucleotide sequences
- 10.1038/s41592-018-0046-7 may be a valid DOI for title: Bioconda: sustainable and comprehensive software distribution for the life sciences

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@akikuno thanks for this submission. I am the AEiC for this track, and here to help with initial steps. Note I have just triggered a scope review by our editorial board. This scope review is to help me determine if this work conforms to our substantial scholarly effort criteria, e.g. in terms of size/maturity/functionality.

This scope review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

Note to editors. This looks like this submission also includes: https://github.com/akikuno/cstag-cli, for which cloc gives us:

github.com/AlDanial/cloc v 1.90  T=0.02 s (555.0 files/s, 24121.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         4             69              0            166
Python                           4             40             18             90
YAML                             3             14              0             68
Bourne Shell                     1             18             18             33
TOML                             1              4              0             27
-------------------------------------------------------------------------------
SUM:                            13            145             36            384
-------------------------------------------------------------------------------

[Kevin-Mattheus-Moerman]

@akikuno I have just removed the query-scope label as I am pleased to inform you this work has passed the initial scope check by our editorial board. I will now assign a handling editor. Note though that the editor I'll assign (@jmschrei) is handling many other submissions and expects to be able to get to this submission within about 2 weeks.

If you'd like to suggest reviewers at this point that would be helpful for us. You can do so by listing their GitHub handles, but please do leave out the @ symbol so they are not tagged.

@akikuno on your repository, I see you have a code-of-conduct, and the README talks about "Feedback and Support" (and posting issues), however, can you also add instructions for users on how to contribute? A detailed way of doing so would be to add a CONTRIBUTING.md file (e.g. see also examples here: https://contributing.md/example/), a more basic approach is to simply spell out some simple instructions in the README.

[Kevin-Mattheus-Moerman]

@editorialbot assign @jmschrei as editor

[editorialbot]

Assigned! @jmschrei is now the editor

[akikuno]

@Kevin-Mattheus-Moerman @jmschrei

I appreciate your feedback. I am very pleased to be able to undergo the review process with JOSS.

As recommended, I have included a CONTRIBUTING.md file in the repository, which can be found here:
https://github.com/akikuno/cstag/blob/main/CONTRIBUTING.md

For potential reviewers, I propose the following individuals:

• Marcus D Sherman, author of Bamnostic,
• Jesse D. Bloom, author of Alignparse,
• Kazuki Nakamae, a known expert in the field of genome editing analysis.

Kind regards,

[jmschrei]

Sorry for the delay, @akikuno. Let's get this going.

@betteridiot, @jbloom, @KazukiNakamae, would any of you be willing to serve as reviewers for this submission, or have suggestions for others that might be able to? Thanks!

[betteridiot]

I would happy to review this.

[jmschrei]

Thanks!

[jmschrei]

@editorialbot add @betteridiot as reviewer

[editorialbot]

@betteridiot added to the reviewers list!

[jbloom]

If another reviewer is needed, I would also be happy to review this. Just let me know.

[jmschrei]

Awesome, thanks!

[jmschrei]

@editorialbot add @jbloom as reviewer

[editorialbot]

@jbloom added to the reviewers list!

[jmschrei]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6066.