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[REVIEW]: delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition #7385

Open editorialbot opened 10 hours ago

editorialbot commented 10 hours ago

Submitting author: !--author-handle-->@bricoletc<!--end-author-handle-- (Brice Letcher) Repository: https://github.com/bricoletc/delfies Branch with paper.md (empty if default branch): Version: v0.6.0 Editor: !--editor-->@mahfuz05062<!--end-editor-- Reviewers: @KatyBrown, @natir Archive: Pending

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status

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Markdown: [![status](https://joss.theoj.org/papers/e9a54b5b34327be54050d6796cf9a31b/status.svg)](https://joss.theoj.org/papers/e9a54b5b34327be54050d6796cf9a31b)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@KatyBrown & @natir, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mahfuz05062 know.

Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest

Checklists

📝 Checklist for @natir

editorialbot commented 10 hours ago

Hello humans, 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 commented 10 hours ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1093/bioinformatics/btab613 is OK
- 10.1093/bioinformatics/btv691 is OK
- 10.1093/gbe/evaa147 is OK
- 10.1093/bioinformatics/btaa226 is OK
- 10.1007/BF00292858 is OK
- 10.1016/0092-8674(91)90077-c is OK
- 10.1111/brv.12796 is OK
- 10.1016/j.tig.2022.02.003 is OK
- 10.1093/nar/gkv416 is OK
- 10.1128/mmbr.00184-22 is OK
- 10.1371/journal.ppat.1011087 is OK
- 10.1016/j.cub.2023.07.058 is OK
- 10.1093/g3journal/jkaa020 is OK
- 10.1016/j.cub.2022.10.043 is OK
- 10.1073/pnas.2115642118 is OK
- 10.1073/pnas.2115635118 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Über Differenzierung der Zellkerne während der Fur...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 10 hours ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1112.8 files/s, 115735.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            212             73           1440
Markdown                         6             82              0            300
TeX                              1             27              0            235
YAML                             2              6              4             68
make                             1             11             10             48
TOML                             1              5              0             30
Bourne Shell                     1             13              8             28
-------------------------------------------------------------------------------
SUM:                            25            356             95           2149
-------------------------------------------------------------------------------

Commit count by author:

   108  Brice Letcher
editorialbot commented 10 hours ago

Paper file info:

📄 Wordcount for paper.md is 951

✅ The paper includes a Statement of need section

editorialbot commented 10 hours ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

mahfuz05062 commented 10 hours ago

@KatyBrown, @natir - Thank you for agreeing to review this submission.

This is the review thread for the paper. All of our communications will happen here from now on.

As mentioned above, you can use the command @editorialbot generate my checklist to create your review checklist. As you go over the submission, please check any items that you feel have been satisfied.

There are also links to the JOSS reviewer guidelines (https://joss.readthedocs.io/en/latest/reviewer_guidelines.html)

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/7385 so that a link is created to this thread for visibility. Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if you require additional time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period.

Please feel free to ping me (@mahfuz05062) if you have any questions/concerns.

editorialbot commented 10 hours ago

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

natir commented 10 hours ago

Review checklist for @natir

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper