[REVIEW]: Rasusa: Randomly subsample sequencing reads to a specified coverage

whedon commented 2 years ago

Submitting author: @mbhall88 (Michael Hall) Repository: https://github.com/mbhall88/rasusa Version: v0.6.1 Editor: @mikldk Reviewer: @k3yavi, @holtgrewe Archive: 10.5281/zenodo.5895111

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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

@k3yavi & @holtgrewe, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @k3yavi

✨ 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

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mbhall88) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @holtgrewe

✨ 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

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mbhall88) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @k3yavi, @holtgrewe it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (345.9 files/s, 86114.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                             5            318            278           1528
Markdown                         2            187              0            516
YAML                             3             40             12            298
TOML                             2              3              1             32
Dockerfile                       1              9              0             14
-------------------------------------------------------------------------------
SUM:                            13            557            291           2388
-------------------------------------------------------------------------------

Statistical information for the repository '7d29f2b8405fd72a4e0460a4' was
gathered on 2021/11/22.
No commited files with the specified extensions were found.

whedon commented 2 years ago

PDF failed to compile for issue #3941 with the following error:

 Can't find any papers to compile :-(

mikldk commented 2 years ago

@whedon check references from branch joss_paper

whedon commented 2 years ago

Attempting to check references... from custom branch joss_paper

whedon commented 2 years ago

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

OK DOIs

- 10.1186/s40793-019-0347-1 is OK
- 10.1186/s12859-018-2445-2 is OK
- 10.1099/mgen.0.000294 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mikldk commented 2 years ago

@whedon generate pdf from branch joss_paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon commented 2 years ago

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

mikldk commented 2 years ago

@k3yavi, @holtgrewe: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

mikldk commented 2 years ago

@k3yavi, @holtgrewe, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

whedon commented 2 years ago

:wave: @k3yavi, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @holtgrewe, please update us on how your review is going (this is an automated reminder).

k3yavi commented 2 years ago

Hi @mikldk , according to JOSS guidelines, I think the paper and the tool passes all the criteria mentioned in the checklist.

I do have some minor points to mention, is it Ok to mention them here or the review is strictly checklist based ?

mikldk commented 2 years ago

@k3yavi Sounds good. Your input would be very valuable. Please create issues in the repo and mention this issue such that they are linked.

mikldk commented 2 years ago

@holtgrewe, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

holtgrewe commented 2 years ago

@mikldk sorry for the delay, will do it over christmas

mikldk commented 2 years ago

@holtgrewe, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

holtgrewe commented 2 years ago

@mikldk I'm starting now.

holtgrewe commented 2 years ago

The invitation link has expired. I'll continue my review anyway now. Let me know how to proceed in the "formal" process.

holtgrewe commented 2 years ago

I could not edit the checklist above. I took the one from the joss docs, below are the fields I filled. I need to actually test the software on Monday.

manuscript

summary

actually also useful for benchmarks

main text

Can review guideline be addressed? "Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it."
The link to the software archive appears to not work.

review considerations

software license: MIT, license file is there
scholarly effort: check
documentation
- statement of need: check
- installation instructions: excellent
- example usage: excellent
- functionality: TODO
- tests: excellent
authorship: check
novelty: check
proprietary software: not applicable

checklist

general

repository URL: OK
license: OK
contribution and authorship: OK

functionality

installation: check
functionality: check
performance: check

documentation

statement of need: check
installation: check
example usage: check
functionality documentation: check
automated tests: check
community guidelines: (1) check, for (2,3): it's a github project with issues, so these work for me - check

software paper

summary: check
statement of need: check
state of the field: check
quality of writing: check
reference: check

mikldk commented 2 years ago

@whedon re-invite @holtgrewe as reviewer

whedon commented 2 years ago

OK, the reviewer has been re-invited.

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

mikldk commented 2 years ago

@holtgrewe Thanks. I just re-invited you. After accept you should be able to check of the boxes. Thanks for your work so far.

holtgrewe commented 2 years ago

@mikldk thanks, installed and tested this morning. Looks all good.

mikldk commented 2 years ago

@k3yavi, @holtgrewe: Thank you for your review.

@mbhall88:

Please have a final read though of the paper, checking language etc.
Have a final check of the proofs with @whedon generate pdf
In general, be sure that all versions are correct and that the repo is in the state that should be published.
Please make a tagged release and archive (e.g. with Zenodo) as described here, and report the version number and archive DOI in this thread. Please verify that the archive deposit has the correct metadata (title and author list), or edit these if that is not the case.

mbhall88 commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #3941 with the following error:

 Can't find any papers to compile :-(

mbhall88 commented 2 years ago

@whedon generate pdf from branch joss_paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon commented 2 years ago

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

mbhall88 commented 2 years ago

@mikldk I am happy with the final proofs.

Regarding the tagged release: I have Zenodo integrated with the repository already, so when I tag a release, a Zenodo archive will be created automatically. Is this fine?

One question before I tag a new release: should I merge the joss_paper branch into the master branch and then tag? That way the paper is included with the release?

mikldk commented 2 years ago

@mbhall88 You don't have to merge the joss_paper branch into the main branch. It's up to you. Please let me know once you have made a release that is accessible at e.g. Zenodo.

mbhall88 commented 2 years ago

Hi @mikldk I have merged joss_paper into master and tagged a release with v0.6.1. It's on Zenodo at https://doi.org/10.5281/zenodo.5895111

mikldk commented 2 years ago

@whedon set 10.5281/zenodo.5895111 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5895111 is the archive.

mikldk commented 2 years ago

@whedon set v0.6.1 as version

whedon commented 2 years ago

OK. v0.6.1 is the version.

mikldk commented 2 years ago

@mbhall88: Can you add "B." initial to Zenodo? (Or remove it from the paper.)

mbhall88 commented 2 years ago

@mbhall88: Can you add "B." initial to Zenodo? (Or remove it from the paper.)

Changed on Zenodo.

mikldk commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.1186/s40793-019-0347-1 is OK
- 10.1186/s12859-018-2445-2 is OK
- 10.1099/mgen.0.000294 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mikldk commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1186/s40793-019-0347-1 is OK
- 10.1186/s12859-018-2445-2 is OK
- 10.1099/mgen.0.000294 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2906

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2906, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

mbhall88 commented 2 years ago

Final proof looks good to me. Do I accept this or do you @mikldk?

mikldk commented 2 years ago

@mbhall88 Neither of us - an EiC will do that when they have checked that everything looks fine.

arfon commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

openjournals / joss-reviews