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[REVIEW]: QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data #5313

Closed editorialbot closed 10 months ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@ManavalanG<!--end-author-handle-- (Manavalan Gajapathy) Repository: https://github.com/uab-cgds-worthey/quac Branch with paper.md (empty if default branch): joss_manuscript Version: 1.6 Editor: !--editor-->@lpantano<!--end-editor-- Reviewers: @brentp, @Redmar-van-den-Berg Archive: 10.5281/zenodo.10002036

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/29354a9f9b0e02ec16fdc08c7c7648a6"><img src="https://joss.theoj.org/papers/29354a9f9b0e02ec16fdc08c7c7648a6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/29354a9f9b0e02ec16fdc08c7c7648a6/status.svg)](https://joss.theoj.org/papers/29354a9f9b0e02ec16fdc08c7c7648a6)

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

@brentp & @Redmar-van-den-Berg, 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 @brentp

📝 Checklist for @Redmar-van-den-Berg

lpantano commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btw354 is OK
- 10.1038/s41436-020-01084-8 is OK
- 10.1038/s41525-020-00154-9 is OK
- 10.1093/bioinformatics/btv566 is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1093/gigascience/gix090 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1101/gr.246934.118 is OK
- 10.1186/s13073-020-00761-2 is OK
- 10.12688/f1000research.15931.2 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 10 months 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/4707, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 10 months ago

@editorialbot set 1.6 as version

editorialbot commented 10 months ago

Done! version is now 1.6

Kevin-Mattheus-Moerman commented 10 months ago

@ManavalanG As EiC on this track I have the honor of helping to process the last steps. I have just checked your repository, this review, the paper, and the archive link, and all seems in order. I will now proceed to accept this work.

Kevin-Mattheus-Moerman commented 10 months ago

@editorialbot accept

editorialbot commented 10 months ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 10 months ago

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: Gajapathy given-names: Manavalan orcid: "https://orcid.org/0000-0002-8606-0113" - family-names: Wilk given-names: Brandon M. orcid: "https://orcid.org/0000-0002-4110-2324" - family-names: Worthey given-names: Elizabeth A. orcid: "https://orcid.org/0000-0003-4083-7764" contact: - family-names: Gajapathy given-names: Manavalan orcid: "https://orcid.org/0000-0002-8606-0113" - family-names: Worthey given-names: Elizabeth A. orcid: "https://orcid.org/0000-0003-4083-7764" doi: 10.5281/zenodo.10002036 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Gajapathy given-names: Manavalan orcid: "https://orcid.org/0000-0002-8606-0113" - family-names: Wilk given-names: Brandon M. orcid: "https://orcid.org/0000-0002-4110-2324" - family-names: Worthey given-names: Elizabeth A. orcid: "https://orcid.org/0000-0003-4083-7764" date-published: 2023-10-23 doi: 10.21105/joss.05313 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 5313 title: "QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05313" volume: 8 title: "QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data" ```

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.

Find more information on .cff files here and here.

editorialbot commented 10 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 10 months ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4716
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05313
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 10 months ago

@ManavalanG congratulations on this JOSS publication!

@lpantano thanks for editing!

And a special thanks to the reviewers: @brentp, @Redmar-van-den-Berg :tada:

editorialbot commented 10 months ago

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05313/status.svg)](https://doi.org/10.21105/joss.05313)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05313">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05313/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05313/status.svg
   :target: https://doi.org/10.21105/joss.05313

This is how it will look in your documentation:

DOI

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