Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[PRE REVIEW]: Koverage: Read-coverage analysis for massive (meta)genomics datasets #6117

Closed
editorialbot opened this issue Dec 4, 2023 · 25 comments
Assignees
Labels
pre-review Python TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode.

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Dec 4, 2023

Submitting author: @beardymcjohnface (Michael J. Roach)
Repository: https://github.com/beardymcjohnface/Koverage
Branch with paper.md (empty if default branch): JOSS
Version: 0.1.7
Editor: @csoneson
Reviewers: @lparsons, @telatin
Managing EiC: Kevin M. Moerman

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3"><img src="https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3/status.svg)](https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3)

Author instructions

Thanks for submitting your paper to JOSS @beardymcjohnface. Currently, there isn't a JOSS editor assigned to your paper.

@beardymcjohnface if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Dec 4, 2023
@editorialbot
Copy link
Collaborator Author

Hello human, 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
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (627.4 files/s, 60366.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            362            341           1609
SVG                              1              1              1            663
Markdown                        10            195              0            545
YAML                            15             43             16            353
TeX                              1              0              0            201
-------------------------------------------------------------------------------
SUM:                            45            601            358           3371
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 2060

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.12688/f1000research.29032.1 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1093/gigascience/giab008 is OK
- 10.25957/FLINDERS.HPC.DEEPTHOUGHT is OK
- 10.1186/s13015-021-00185-6 is OK
- 10.1089/cmb.2022.0262 is OK
- 10.1101/2023.04.19.537311 is OK
- 10.1007/s00248-022-02094-6 is OK
- 10.1093/bioinformatics/btad586 is OK
- 10.1101/2022.05.15.492003 is OK

MISSING DOIs

- 10.31219/osf.io/8w5j3 may be a valid DOI for title: Ten simple rules and a template for creating workflows-as-applications

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

Five most similar historical JOSS papers:

Bam-readcount - rapid generation of basepair-resolution sequence metrics
Submitting author: @chrisamiller
Handling editor: @lpantano (Active)
Reviewers: @friedue, @bebatut
Similarity score: 0.8463

Rasusa: Randomly subsample sequencing reads to a specified coverage
Submitting author: @mbhall88
Handling editor: @mikldk (Retired)
Reviewers: @k3yavi, @holtgrewe
Similarity score: 0.8434

covtobed: a simple and fast tool to extract coverage tracks from BAM files
Submitting author: @telatin
Handling editor: @will-rowe (Retired)
Reviewers: @jdeligt, @brentp
Similarity score: 0.8356

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences
Submitting author: @warrenlr
Handling editor: @biorelated (Retired)
Reviewers: @andrewjpage
Similarity score: 0.8284

reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome
Submitting author: @nterhoeven
Handling editor: @mgymrek (Retired)
Reviewers: @jsgalan
Similarity score: 0.8272

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Dec 4, 2023
beardymcjohnface added a commit to beardymcjohnface/Koverage that referenced this issue Dec 4, 2023
@beardymcjohnface
Copy link

Author instructions
@beardymcjohnface if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Some potential reviewers matching Python and workflow/pipeline that I believe would be suitable.

  • rcannood
  • lparsons
  • telatin
  • camillescott
  • ManavalanG
  • jmcbroome

@Kevin-Mattheus-Moerman
Copy link
Member

@editorialbot invite @csoneson as editor

@editorialbot
Copy link
Collaborator Author

Invitation to edit this submission sent!

@csoneson
Copy link
Member

@editorialbot assign @csoneson as editor

@editorialbot
Copy link
Collaborator Author

Assigned! @csoneson is now the editor

@csoneson
Copy link
Member

👋🏻 @beardymcjohnface - I will handle your submission, and start by finding at least two suitable reviewers. Thanks for the suggestions above!

@csoneson
Copy link
Member

👋🏻 @camillescott, @lparsons, @jmcbroome - would you be interested in reviewing this submission for the Journal of Open Source Software (JOSS)?

Koverage: Read-coverage analysis for massive (meta)genomics datasets
#6117

Thanks in advance!

@lparsons
Copy link

lparsons commented Jan 12, 2024 via email

@csoneson
Copy link
Member

Thanks @lparsons! Once we have secured one more reviewer I will open the review issue.

@csoneson
Copy link
Member

@editorialbot add @lparsons as reviewer

@editorialbot
Copy link
Collaborator Author

@lparsons added to the reviewers list!

@csoneson
Copy link
Member

👋🏻 @ManavalanG, @telatin - would one of you be interested in reviewing this submission for the Journal of Open Source Software (JOSS)?

Koverage: Read-coverage analysis for massive (meta)genomics datasets
#6117

Thanks in advance!

@telatin
Copy link

telatin commented Jan 16, 2024

I can, starting from Jan 22. Happy to wait and see if someone else can offer a swifter review

@csoneson
Copy link
Member

Thank you @telatin! Let's give it another day and see, but starting Jan 22 would not be a problem at all.

@csoneson
Copy link
Member

👋🏻 @telatin - I would be happy to take you up on your offer here, and will assign you as a reviewer with the understanding that you will not start before Jan 22. Thanks!

@csoneson
Copy link
Member

@editorialbot add @telatin as reviewer

@editorialbot
Copy link
Collaborator Author

@telatin added to the reviewers list!

@csoneson
Copy link
Member

@editorialbot start review

@editorialbot
Copy link
Collaborator Author

OK, I've started the review over in #6235.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
pre-review Python TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode.
Projects
None yet
Development

No branches or pull requests

6 participants