[REVIEW]: Back to sequences: find the origin of k-mers #7066

editorialbot · 2024-08-01T19:28:12Z

Submitting author: @pierrepeterlongo (Pierre Peterlongo)
Repository: https://github.com/pierrepeterlongo/back_to_sequences/
Branch with paper.md (empty if default branch):
Version: v0.6.6
Editor: @majensen
Reviewers: @Anjan-Purkayastha, @amoeba
Archive: 10.5281/zenodo.13794732

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21"><img src="https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21/status.svg)](https://joss.theoj.org/papers/2b20d0fa287109fb0fcdb39b48b81b21)

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

@Anjan-Purkayastha & @amoeba, 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:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @majensen 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 @Anjan-Purkayastha

📝 Checklist for @amoeba

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-08-01T19:28:15Z

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editorialbot · 2024-08-01T19:28:31Z

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

OK DOIs

- 10.1186/s13059-022-02771-2 is OK
- 10.1038/nmeth.1376 is OK
- 10.1101/gr.101360.109 is OK
- 10.7717/peerj-cs.94 is OK
- 10.1093/bfgp/elr035 is OK
- 10.1186/s13059-019-1632-4 is OK
- 10.1093/bioinformatics/btu288 is OK
- 10.1093/nar/gku1187 is OK
- 10.1093/bioadv/vbac029 is OK
- 10.1101/gr.277615.122 is OK
- 10.1145/585265.585267 is OK
- 10.1089/cmb.2012.0021 is OK
- 10.1016/j.dam.2018.03.035 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.1038/s41579-020-0364-5 is OK
- 10.1093/bioinformatics/btac689 is OK
- 10.1186/s12864-015-1406-7 is OK
- 10.1016/j.isci.2023.108057 is OK

MISSING DOIs

- No DOI given, and none found for title: The Platinum Searcher
- No DOI given, and none found for title: The Silver Searcher
- No DOI given, and none found for title: Kmer Mapper
- No DOI given, and none found for title: AHash: A Load-Balanced One Permutation Hash

INVALID DOIs

- None

editorialbot · 2024-08-01T19:28:37Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1554.0 files/s, 235858.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                            11            357            216           1792
CSV                              3              0              0           1497
Markdown                         6            118              0            469
TeX                              1             26              3            216
Python                           6             50             37            152
Bourne Shell                     4             38             23            144
YAML                             3             17              0            102
TOML                             1             12              5             38
-------------------------------------------------------------------------------
SUM:                            35            618            284           4410
-------------------------------------------------------------------------------

Commit count by author:

   134	Pierre Peterlongo
    14	Pierre Marijon
    10	Anthony Baire
     7	PETERLONGO Pierre
     1	Francesco Andreace

editorialbot · 2024-08-01T19:28:45Z

Paper file info:

📄 Wordcount for paper.md is 2348

✅ The paper includes a Statement of need section

editorialbot · 2024-08-01T19:28:47Z

License info:

🟡 License found: GNU Affero General Public License v3.0 (Check here for OSI approval)

editorialbot · 2024-08-01T19:29:54Z

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

Anjan-Purkayastha · 2024-08-01T22:40:15Z

Review checklist for @Anjan-Purkayastha

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/pierrepeterlongo/back_to_sequences/?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@pierrepeterlongo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

majensen · 2024-08-12T18:10:09Z

@Anjan-Purkayastha @amoeba thanks for agreeing to review. Let me know if there are any blockers for you. Mark

amoeba · 2024-08-12T18:14:52Z

Hey @majensen, I can have my review in by Aug 18 if that timeline works.

editorialbot · 2024-08-17T06:46:01Z

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

editorialbot · 2024-08-19T05:14:35Z

I'm sorry @Anjan-Purkayastha, I'm afraid I can't do that. That's something only editors are allowed to do.

Anjan-Purkayastha · 2024-08-19T05:22:41Z

@majensen: Have completed installing and testing the tool. It is a useful addition to the set of general-purpose bioinformatics tools we use for processing NGS data.
I have left some good enhancement suggestion at this link, for the authors. Aside from this, they need to update their citations, and they should be good to go.
This is my first time interacting over GitHub, please do let me know if there is anything else I need to do to complete this review. Cheers.

majensen · 2024-08-19T16:42:42Z

Thanks very much @Anjan-Purkayastha -

amoeba · 2024-08-20T02:11:36Z

Review checklist for @amoeba

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/pierrepeterlongo/back_to_sequences/?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@pierrepeterlongo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

amoeba · 2024-08-20T04:08:51Z

Hi @majensen and @pierrepeterlongo, I've finished my review and filed an issue on your repo. I do ask for some changes there so please have a look and let me know when you'd like me to re-review.

majensen · 2024-08-25T03:21:07Z

Hi @pierrepeterlongo - the reviewers have made their comments and have items to address at pierrepeterlongo/back_to_sequences#6 and pierrepeterlongo/back_to_sequences#8. Please keep us informed on your progress here as you work through these. Thanks!

pierrepeterlongo · 2024-08-26T14:16:40Z

Hi @majensen
Thanks a lot for your message. I'm planning to apply the (nice) recommendations by the end of the week.

Pierre

pierrepeterlongo · 2024-08-27T08:50:34Z

@editorialbot generate pdf

editorialbot · 2024-08-27T08:52:17Z

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

pierrepeterlongo · 2024-08-27T14:43:05Z

Hello @majensen,

We took in consideration reviewer's comments. I closed the related issues. pierrepeterlongo/back_to_sequences#6 and pierrepeterlongo/back_to_sequences#8.

Best,
Pierrre

majensen · 2024-08-28T01:19:37Z

Thanks @pierrepeterlongo - I am fine with your solution regarding the length of the paper (I tend to be lenient on this aspect). @amoeba @Anjan-Purkayastha if you would have a look this week that would be excellent.
Thanks!

editorialbot · 2024-09-19T16:19:46Z

Done! version is now 0.6.6

pierrepeterlongo · 2024-09-19T16:23:49Z

One minor update @pierrepeterlongo - can you make the title of the repo https://doi.org/10.5281/zenodo.13794732 the same as that of the paper, ie "Back to sequences: find the origin of k-mers"? This is something JOSS requires.

Done :)

majensen · 2024-09-20T00:57:52Z

@editorialbot recommend-accept

editorialbot · 2024-09-20T00:57:54Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-09-20T00:58:17Z

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

✅ OK DOIs

- 10.1186/s13059-022-02771-2 is OK
- 10.1038/nmeth.1376 is OK
- 10.1101/gr.101360.109 is OK
- 10.7717/peerj-cs.94 is OK
- 10.1093/bfgp/elr035 is OK
- 10.1186/s13059-019-1632-4 is OK
- 10.1093/bioinformatics/btu288 is OK
- 10.1093/nar/gku1187 is OK
- 10.1093/bioadv/vbac029 is OK
- 10.1101/gr.277615.122 is OK
- 10.1145/585265.585267 is OK
- 10.1089/cmb.2012.0021 is OK
- 10.1016/j.dam.2018.03.035 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.1038/s41579-020-0364-5 is OK
- 10.1093/bioinformatics/btac689 is OK
- 10.1186/s12864-015-1406-7 is OK
- 10.1016/j.isci.2023.108057 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The Platinum Searcher
- No DOI given, and none found for title: The Silver Searcher
- No DOI given, and none found for title: Kmer Mapper
- No DOI given, and none found for title: AHash: A Load-Balanced One Permutation Hash

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-09-20T00:59:49Z

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5895, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2024-09-20T05:21:57Z

I'm sorry @pierrepeterlongo, I'm afraid I can't do that. That's something only eics are allowed to do.

majensen · 2024-09-20T20:38:01Z

@pierrepeterlongo - I should explain that I as the topic editor do the "recommend-accept" command, which does some checks and then informs the Editors-in-chief. One of them will come soon and do a final check - they may have questions or minor fixes. When they are satisfied, they'll push the big button that publishes the paper officially.
Thanks!

pierrepeterlongo · 2024-09-20T20:57:12Z

Yep this is what I understood, a bit late :)

Kevin-Mattheus-Moerman · 2024-09-23T09:33:44Z

Kevin-Mattheus-Moerman · 2024-09-23T09:33:54Z

@editorialbot set v0.6.6 as version

editorialbot · 2024-09-23T09:33:57Z

Done! version is now v0.6.6

pierrepeterlongo · 2024-09-23T13:17:46Z

Hello.

I also changed the zenodo version label from 0.6.6 to v0.6.6

https://zenodo.org/records/13794732

Kevin-Mattheus-Moerman · 2024-09-23T14:17:24Z

@editorialbot accept

editorialbot · 2024-09-23T14:17:27Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-09-23T14:24:41Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Baire
  given-names: Anthony
- family-names: Marijon
  given-names: Pierre
  orcid: "https://orcid.org/0000-0002-6694-6873"
- family-names: Andreace
  given-names: Francesco
  orcid: "https://orcid.org/0009-0008-0566-200X"
- family-names: Peterlongo
  given-names: Pierre
  orcid: "https://orcid.org/0000-0003-0776-6407"
doi: 10.5281/zenodo.13794732
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Baire
    given-names: Anthony
  - family-names: Marijon
    given-names: Pierre
    orcid: "https://orcid.org/0000-0002-6694-6873"
  - family-names: Andreace
    given-names: Francesco
    orcid: "https://orcid.org/0009-0008-0566-200X"
  - family-names: Peterlongo
    given-names: Pierre
    orcid: "https://orcid.org/0000-0003-0776-6407"
  date-published: 2024-09-23
  doi: 10.21105/joss.07066
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7066
  title: "Back to sequences: Find the origin of k-mers"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07066"
  volume: 9
title: "Back to sequences: Find the origin of $k$-mers"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

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editorialbot · 2024-09-23T14:24:45Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-09-23T14:24:46Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07066 joss-papers#5902
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07066
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

majensen · 2024-09-23T18:55:51Z

Congrats @pierrepeterlongo and thanks so much for the reviews @amoeba and @Anjan-Purkayastha !

pierrepeterlongo · 2024-09-23T19:09:22Z

Thank you all. I was a great experience to submit this work to JOSS.

pierrepeterlongo · 2024-09-23T19:42:13Z

Just a last comment, if it is possible, maybe remove the '$'s in the title on the JOSS page:

Kevin-Mattheus-Moerman · 2024-09-26T12:48:02Z

@openjournals/dev @arfon how do we go about removing those dollar symbols? ☝️

xuanxu · 2024-09-28T12:48:07Z

Updated!

pierrepeterlongo · 2024-09-28T20:39:33Z

Perfect, thanks!

Kevin-Mattheus-Moerman · 2024-09-30T09:55:05Z

Great, since that is all set we are good to close this review.

Congratulations @pierrepeterlongo on this JOSS publication!

Thanks @majensen for editing!

And a special thank you to the reviewers: @Anjan-Purkayastha, @amoeba !!

editorialbot · 2024-09-30T09:55:08Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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editorialbot added Python review Rust Shell TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Aug 1, 2024

editorialbot assigned majensen Aug 1, 2024

editorialbot mentioned this issue Aug 1, 2024

[PRE REVIEW]: Back to sequences: find the origin of k-mers #6872

Closed

amoeba mentioned this issue Aug 20, 2024

JOSS Review pierrepeterlongo/back_to_sequences#8

Closed

2 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 20, 2024

editorialbot added accepted published Papers published in JOSS labels Sep 23, 2024

Kevin-Mattheus-Moerman closed this as completed Sep 30, 2024

[REVIEW]: Back to sequences: find the origin of k-mers #7066

[REVIEW]: Back to sequences: find the origin of k-mers #7066

Comments

editorialbot commented Aug 1, 2024 • edited Loading

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Anjan-Purkayastha commented Aug 1, 2024 • edited Loading

Review checklist for @Anjan-Purkayastha

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

majensen commented Aug 12, 2024

amoeba commented Aug 12, 2024

editorialbot commented Aug 17, 2024

editorialbot commented Aug 19, 2024

Anjan-Purkayastha commented Aug 19, 2024

majensen commented Aug 19, 2024

amoeba commented Aug 20, 2024 • edited Loading

Review checklist for @amoeba

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

amoeba commented Aug 20, 2024

majensen commented Aug 25, 2024

pierrepeterlongo commented Aug 26, 2024

pierrepeterlongo commented Aug 27, 2024

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pierrepeterlongo commented Aug 27, 2024

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majensen commented Sep 20, 2024

pierrepeterlongo commented Sep 20, 2024

Kevin-Mattheus-Moerman commented Sep 23, 2024 • edited Loading

Checks on repository

Checks on review issue

Checks on archive

Checks on paper

Remaining points:

Kevin-Mattheus-Moerman commented Sep 23, 2024

editorialbot commented Sep 23, 2024

pierrepeterlongo commented Sep 23, 2024

Kevin-Mattheus-Moerman commented Sep 23, 2024

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majensen commented Sep 23, 2024

pierrepeterlongo commented Sep 23, 2024

pierrepeterlongo commented Sep 23, 2024

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xuanxu commented Sep 28, 2024 • edited Loading

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