[REVIEW]: ROCK: digital normalization of whole genome sequencing data #3790

whedon · 2021-10-01T14:05:06Z

Submitting author: @alex2cris (alexis criscuolo)
Repository: https://gitlab.pasteur.fr/vlegrand/ROCK
Branch with paper.md (empty if default branch):
Version: v_1.9.6
Editor: @luizirber
Reviewers: @hiraksarkar, @ctb
Archive: 10.5281/zenodo.6527091

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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

@hiraksarkar and @ctb, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

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Review checklist for @hiraksarkar

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@alex2cris) 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

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 and who the target audience is?
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?

Review checklist for @ctb

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@alex2cris) 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

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 and who the target audience is?
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?

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

whedon · 2021-10-01T14:05:09Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hiraksarkar it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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whedon · 2021-10-01T14:05:19Z

Wordcount for paper.md is 1929

whedon · 2021-10-01T14:05:22Z

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

OK DOIs

- 10.1016/j.ygeno.2013.07.011 is OK
- 10.12688/f1000research.6924.1 is OK
- 10.1016/j.jalgor.2003.12.001 is OK
- 10.1038/s41598-019-41502-9 is OK
- 10.3390/electronics8070779 is OK
- 10.1093/bioinformatics/btw832 is OK
- 10.1186/s12859-017-1724-7 is OK
- 10.1371/journal.pone.0101271 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-10-01T14:05:22Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (790.7 files/s, 249304.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Bourne Shell                     9            811           1638           7333
C++                             18            670            773           2647
m4                               2            108             22            976
C/C++ Header                    16            394            389            739
Markdown                         2             92              0            212
TeX                              1             10              0             91
make                             4             23              2             54
YAML                             1              3              0             25
XML                              1              0              0             15
-------------------------------------------------------------------------------
SUM:                            54           2111           2824          12092
-------------------------------------------------------------------------------


Statistical information for the repository '315a86ea502d500069586c0d' was
gathered on 2021/10/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Nicolas Joly                     7            36             16            0.23
Veronique Legrand              166         15790           6409           99.76
Véronique Legrand                1             1              1            0.01

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Veronique Legrand          5612           35.5         31.4               25.41

whedon · 2021-10-01T14:05:38Z

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

kyleniemeyer · 2021-10-01T15:02:35Z

@whedon add @ctb as reviewer

whedon · 2021-10-01T15:02:40Z

OK, @ctb is now a reviewer

kyleniemeyer · 2021-10-01T15:04:14Z

@luizirber FYI, if the missing reviewer thing ever happens again, you can just give the add command here, then you need to manually edit whedon's initial comment to add the missing reviewer checklist

alex2cris · 2021-10-01T16:46:34Z

@VeroniqueLegrand @tkergrohen the ROCK [REVIEW] issue is here now

whedon · 2021-10-15T14:05:28Z

👋 @hiraksarkar, please update us on how your review is going (this is an automated reminder).

hiraksarkar · 2021-10-15T23:28:17Z

Hi @luizirber , it seems this invitation https://github.com/openjournals/joss-reviews/invitations is expired, do I need to click on this to edit the checklist? or Should I open a new issue?

arfon · 2021-10-18T06:53:45Z

@whedon re-invite @hiraksarkar as reviewer

whedon · 2021-10-18T06:53:49Z

OK, the reviewer has been re-invited.

@hiraksarkar please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

arfon · 2021-10-18T06:54:09Z

Could you try again now please @hiraksarkar?

alex2cris · 2021-12-09T23:21:08Z

@whedon generate pdf

whedon · 2021-12-09T23:21:39Z

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

alex2cris · 2022-01-24T17:52:49Z

@whedon generate pdf

whedon · 2022-01-24T17:53:23Z

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

arfon · 2022-02-27T18:21:56Z

👋 @hiraksarkar, @ctb – looks like we're waiting on your reviews here. Do you think you could complete your initial reviews in the next couple of weeks?

ctb · 2022-02-28T16:08:18Z

yep, will get on it.

hiraksarkar · 2022-05-06T18:36:56Z

@luizirber I completed my review, and all my raised issues are addressed

Installation: Does installation proceed as outlined in the documentation? https://gitlab.pasteur.fr/vlegrand/ROCK/-/issues/1
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). https://gitlab.pasteur.fr/vlegrand/ROCK/-/issues/1
Another installation problem solved from the issue raised https://gitlab.pasteur.fr/vlegrand/ROCK/-/issues/3

Very nicely executed work. Amazing job by the authors. I am unable to correct the checklist here. The completed checklist is here.

luizirber · 2022-05-06T23:35:03Z

@editorialbot generate pdf

editorialbot · 2022-05-06T23:36:21Z

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

luizirber · 2022-05-06T23:47:43Z

@alex2cris can you please cut a new DOI for archival and report

version number
archive DOI

(almost done! so close!)

luizirber · 2022-05-06T23:49:14Z

@editorialbot check references

editorialbot · 2022-05-06T23:49:19Z

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

OK DOIs

- 10.1016/j.ygeno.2013.07.011 is OK
- 10.12688/f1000research.6924.1 is OK
- 10.1016/j.jalgor.2003.12.001 is OK
- 10.1038/s41598-019-41502-9 is OK
- 10.3390/electronics8070779 is OK
- 10.1093/bioinformatics/btw832 is OK
- 10.1186/s12859-017-1724-7 is OK
- 10.1371/journal.pone.0101271 is OK

MISSING DOIs

- None

INVALID DOIs

- None

alex2cris · 2022-05-07T13:13:37Z

Dear @luizirber

The current version is: 1.9.6
This version is tagged in the gitlab repository (https://gitlab.pasteur.fr/vlegrand/ROCK)

I also made a DOI for this version at Zenodo: 10.5281/zenodo.6527091
(https://zenodo.org/record/6527091)

Hope that everything is ok.

Best regards,

-- Alexis --

alex2cris · 2022-05-07T13:15:44Z

@whedon generate pdf

editorialbot · 2022-05-07T13:15:45Z

My name is now @editorialbot

alex2cris · 2022-05-07T13:16:41Z

@editorialbot generate pdf

editorialbot · 2022-05-07T13:18:00Z

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

luizirber · 2022-05-07T15:45:41Z

@editorialbot set 10.5281/zenodo.6527091 as archive

editorialbot · 2022-05-07T15:45:43Z

Done! Archive is now 10.5281/zenodo.6527091

luizirber · 2022-05-07T15:46:41Z

@editorialbot set v_1.9.6 as version

editorialbot · 2022-05-07T15:46:43Z

Done! version is now v_1.9.6

luizirber · 2022-05-07T15:50:15Z

@editorialbot recommend-accept

editorialbot · 2022-05-07T15:50:16Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-05-07T15:50:20Z

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

OK DOIs

- 10.1016/j.ygeno.2013.07.011 is OK
- 10.12688/f1000research.6924.1 is OK
- 10.1016/j.jalgor.2003.12.001 is OK
- 10.1038/s41598-019-41502-9 is OK
- 10.3390/electronics8070779 is OK
- 10.1093/bioinformatics/btw832 is OK
- 10.1186/s12859-017-1724-7 is OK
- 10.1371/journal.pone.0101271 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-05-07T15:52:02Z

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

Check final proof 👉 openjournals/joss-papers#3204

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3204, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2022-05-07T21:19:49Z

@editorialbot accept

editorialbot · 2022-05-07T21:19:50Z

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

editorialbot · 2022-05-07T21:21:16Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-05-07T21:21:17Z

🚨🚨🚨 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.03790 joss-papers#3205
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03790
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2022-05-07T21:24:30Z

Congratulations @alex2cris on your article's publication in JOSS!

Many thanks to @hiraksarkar and @ctb for reviewing this, and @luizirber for editing.

editorialbot · 2022-05-07T21:24:31Z

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

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Markdown:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03790/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03790/status.svg
   :target: https://doi.org/10.21105/joss.03790

This is how it will look in your documentation:

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whedon added M4 Makefile review Shell labels Oct 1, 2021

whedon assigned luizirber Oct 1, 2021

whedon mentioned this issue Oct 1, 2021

[PRE REVIEW]: ROCK: digital normalization of whole genome sequencing data #3684

Closed

whedon assigned ctb and luizirber and unassigned luizirber Oct 1, 2021

whedon assigned hiraksarkar Oct 16, 2021

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 7, 2022

editorialbot added accepted published Papers published in JOSS labels May 7, 2022

kyleniemeyer closed this as completed May 7, 2022

editorialbot mentioned this issue Jun 24, 2024

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

Closed

[REVIEW]: ROCK: digital normalization of whole genome sequencing data #3790

[REVIEW]: ROCK: digital normalization of whole genome sequencing data #3790

Comments

whedon commented Oct 1, 2021 • edited by editorialbot Loading

Status

Reviewer instructions & questions

Review checklist for @hiraksarkar

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ctb

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Oct 1, 2021

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alex2cris commented Oct 1, 2021

whedon commented Oct 15, 2021

hiraksarkar commented Oct 15, 2021

arfon commented Oct 18, 2021

whedon commented Oct 18, 2021

arfon commented Oct 18, 2021

alex2cris commented Dec 9, 2021

whedon commented Dec 9, 2021

alex2cris commented Jan 24, 2022

whedon commented Jan 24, 2022

arfon commented Feb 27, 2022

ctb commented Feb 28, 2022

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edited by editorialbot

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