[REVIEW]: RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@cagret@lpantano<!--end-editor-- Reviewers: @swatimanekar, @samhorsfield96 Archive: 10.6084/m9.figshare.21711767

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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

@swatimanekar & @samhorsfield96, 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 @lpantano 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 @swatimanekar

📝 Checklist for @samhorsfield96

samhorsfield96 commented 1 year ago

Hi @lpantano, I have updated the checklist. The one final area is Quality of writing - There is an error with the formatting of the name "A. thaliana". Apart from this I am happy to accept the paper.

cagret commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

cagret commented 1 year ago

A. Thaliana should be in italics i'll fix this

cagret commented 1 year ago

Test A.Thaliana

lpantano commented 1 year ago

Thank you @cagret, @samhorsfield96. @swatimanekar could you update us with the current status of you review please.

lpantano commented 1 year ago

@cagret, I am taking care of the last three @swatimanekar's items were unchecked. The statement of need is there. I went over the documentation. In the readme file, there is something missing here:

SGE command example obtained with MakeQsubYaml.sh script:

Last thing, can you add to the readme an example of the output. With that I think I can check that part and proceed with publication. Thanks

lpantano commented 1 year ago

Hi @cagret, do you think you can make this small change to address my comment, then we can proceed with acceptance? thanks

cagret commented 1 year ago

Hello I updated the readme file with an example. Let me know if it's ok for you. Please excuse me for the delay I have a lot of projects right now.

lpantano commented 1 year ago

thank you, no problem. It is been busy here as well. Last edit: in line 211 shows an empty code, can you fix that, please?

cagret commented 1 year ago

Fixed

lpantano commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

lpantano commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1093/bib/bbw089 is OK
- 10.1111/pbi.12499 is OK
- 10.1093/gigascience/giy125 is OK
- 10.1093/nar/gkp492 is OK
- 10.1186/1471-2105-12-242 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1137/070685531 is OK
- 10.1007/978-3-540-30218-6_19 is OK
- 10.1016/S0020-0255(01)00098-6 is OK
- 10.1109/DCC.2016.17 is OK
- 10.1093/bioinformatics/btu756 is OK
- 10.1093/bioinformatics/btv603 is OK
- 10.1186/s13015-016-0083-7 is OK
- 10.1093/bioinformatics/btw609 is OK
- 10.1137/0222058 is OK
- 10.1093/bioinformatics/btt460 is OK
- 10.1371/journal.pone.0109384 is OK
- 10.1186/s13015-016-0066-8 is OK
- 10.1007/978-3-642-03784-9_7 is OK
- 10.4230/OASIcs.GCB.2013.35 is OK
- 10.1186/s12864-017-4401-3 is OK
- 10.1007/978-3-319-38851-9_22 is OK
- 10.1089/cmb.2017.0258 is OK
- 10.1093/bioinformatics/btz162 is OK
- 10.1038/nature11346 is OK
- 10.1038/s41588-018-0041-z is OK
- 10.1038/sdata.2018.79 is OK
- 10.1186/2047-217X-3-8 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1007/978-3-642-39053-1\_42 URL is INVALID

lpantano commented 1 year ago

@cagret, last detail, could you fix that DOI, please?

cagret commented 1 year ago

i'm on it (:

cagret commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1093/bib/bbw089 is OK
- 10.1111/pbi.12499 is OK
- 10.1093/gigascience/giy125 is OK
- 10.1093/nar/gkp492 is OK
- 10.1186/1471-2105-12-242 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1137/070685531 is OK
- 10.1007/978-3-540-30218-6_19 is OK
- 10.1016/S0020-0255(01)00098-6 is OK
- 10.1007/978-3-642-39053-1_42 is OK
- 10.1109/DCC.2016.17 is OK
- 10.1093/bioinformatics/btu756 is OK
- 10.1093/bioinformatics/btv603 is OK
- 10.1186/s13015-016-0083-7 is OK
- 10.1093/bioinformatics/btw609 is OK
- 10.1137/0222058 is OK
- 10.1093/bioinformatics/btt460 is OK
- 10.1371/journal.pone.0109384 is OK
- 10.1186/s13015-016-0066-8 is OK
- 10.1007/978-3-642-03784-9_7 is OK
- 10.4230/OASIcs.GCB.2013.35 is OK
- 10.1186/s12864-017-4401-3 is OK
- 10.1007/978-3-319-38851-9_22 is OK
- 10.1089/cmb.2017.0258 is OK
- 10.1093/bioinformatics/btz162 is OK
- 10.1038/nature11346 is OK
- 10.1038/s41588-018-0041-z is OK
- 10.1038/sdata.2018.79 is OK
- 10.1186/2047-217X-3-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

cagret commented 1 year ago

fixed

lpantano commented 1 year ago

Thanks, at this point could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

cagret commented 1 year ago

The tagged release is v0.1.5. The arcive is reviewed here : https://figshare.com/articles/software/Redoak-0_1_5_rar/21711767 The DOI : 10.6084/m9.figshare.21711767

lpantano commented 1 year ago

@editorialbot set v0.1.5 as version

editorialbot commented 1 year ago

Done! version is now v0.1.5

lpantano commented 1 year ago

@editorialbot set 10.6084/m9.figshare.21711767 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.6084/m9.figshare.21711767

lpantano commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1093/bib/bbw089 is OK
- 10.1111/pbi.12499 is OK
- 10.1093/gigascience/giy125 is OK
- 10.1093/nar/gkp492 is OK
- 10.1186/1471-2105-12-242 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1137/070685531 is OK
- 10.1007/978-3-540-30218-6_19 is OK
- 10.1016/S0020-0255(01)00098-6 is OK
- 10.1007/978-3-642-39053-1_42 is OK
- 10.1109/DCC.2016.17 is OK
- 10.1093/bioinformatics/btu756 is OK
- 10.1093/bioinformatics/btv603 is OK
- 10.1186/s13015-016-0083-7 is OK
- 10.1093/bioinformatics/btw609 is OK
- 10.1137/0222058 is OK
- 10.1093/bioinformatics/btt460 is OK
- 10.1371/journal.pone.0109384 is OK
- 10.1186/s13015-016-0066-8 is OK
- 10.1007/978-3-642-03784-9_7 is OK
- 10.4230/OASIcs.GCB.2013.35 is OK
- 10.1186/s12864-017-4401-3 is OK
- 10.1007/978-3-319-38851-9_22 is OK
- 10.1089/cmb.2017.0258 is OK
- 10.1093/bioinformatics/btz162 is OK
- 10.1038/nature11346 is OK
- 10.1038/s41588-018-0041-z is OK
- 10.1038/sdata.2018.79 is OK
- 10.1186/2047-217X-3-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3801, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 year ago

@cagret I am the AEiC for this track and here to help process the final steps for acceptance. I have reviewed the archive link and the paper and have the below minor comments:

[x] Change licence to license.
[x] This sentence seems broken: However, we did not use it because in the output, _k_-mers are in "fairly pseudo-random" order and "no guarantee is made about the actual randomness of this order"Documentation of Jellfish, I am guessing Jellfish should be JellyFish, and that order"Documentation of should be rephrased/fixed to, e.g. leading to (feel free to propose an alternative sentence):

However, we did not use it because in the output, k-mers are in "fairly pseudo-random", order and "no guarantee is made about the actual randomness of this order" (see the Jellyfish documentation).
[x] Change softwares to software.
[x] Suggestion (not required): It is customary to use code style formatting for software project names (such as RedOad, JellyFish, OpenMP.,...) in JOSS papers e.g. make use of the "`" symbols in the markdown text e.g. :
```
`RedOak`
```
[x] Suggestion (not required):, on the archive link the description says This paper presents RedOak..... I would probably rephrase that text so it is a description of the project/software rather than making it sound like what is shared is a paper.

cagret commented 1 year ago

Hi, Thank you for your feedback. I have applied all the patches except Jellyfish in JellyFish because in the documentation: https://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf G. Marcais and C. Kingsford use "Jellyfish".

cagret commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/3851
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04363
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 year ago

@cagret congratulations on this publication on JOSS!

@lpantano thank you for editing this work!

And a special thanks to the reviewers: @swatimanekar, @samhorsfield96 !!!!!

editorialbot commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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