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

[editorialbot]

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

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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]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[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.

[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 https://github.com/openjournals/joss-reviews/issues/6066.