[PRE REVIEW]: Step-mothur: Nextflow-Based Quality Control and Filtering Pipeline for Highly Multiplexed Amplicon Sequencing Data

[editorialbot]

Submitting author: @jinfinance (Rong Jin)
Repository: https://github.com/ncezid-biome/HMAS-QC-Pipeline2
Branch with paper.md (empty if default branch): main
Version: v1.2.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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Markdown: [![status](https://joss.theoj.org/papers/764112acf1eb1e09b50ed649be9177ce/status.svg)](https://joss.theoj.org/papers/764112acf1eb1e09b50ed649be9177ce)

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

OK DOIs

- 10.1038/nbt.3820 is OK
- 10.1128/AEM.01541-09 is OK
- 10.1038/s41587-019-0209-9 is OK
- 10.1101/081257 is OK
- 10.7717/peerj.2584 is OK
- 10.14806/ej.17.1.200 is OK
- 10.1093/bioinformatics/btt593 is OK
- 10.1093/bioinformatics/btw354 is OK

MISSING DOIs

- No DOI given, and none found for title: FastQC

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (635.6 files/s, 41688.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            184            183            383
Markdown                         2             44              0            128
TeX                              1              9              0             92
YAML                             3              8              6             77
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            17            245            189            681
-------------------------------------------------------------------------------

Commit count by author:

    61	Jin
     3	Rong Jin
     2	Andrew Huang

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1049

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

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[Kevin-Mattheus-Moerman]

@jinfinance Dear author(s), thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
• In the paper, please do not use country acronyms, so spell out country names.
• The above code report, quoting "lines of code" counts, excludes your Nextflow .nf files. Would you be able to provide an estimate for us here in terms of lines of Nextflow code in your project? Thanks!

[Kevin-Mattheus-Moerman]

@jinfinance note I've just waitlisted this submission as our editors in this domain are currently busy handling other submissions. We'll assign an editor once one becomes available.

[jinfinance]

Thank you, Kevin * I have included a CONTRIBUTING.md and added a link in the README per your request * I have changed the country acronyms (U.S.) in the paper * There are total 10 Nextflow .nf files and I counted (wc -l) total 354 lines of Nextflow code in the project Let me know if you have any further questions. Best, Rong From: Kevin Mattheus Moerman ***@***.***> Sent: Thursday, July 18, 2024 5:29 AM To: openjournals/joss-reviews ***@***.***> Cc: Jin, Rong (CDC/NCEZID/DFWED/EDLB) ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: Step-mothur: Nextflow-Based Quality Control and Filtering Pipeline for Highly Multiplexed Amplicon Sequencing Data (Issue #6958) CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

…

________________________________ @jinfinance<https://github.com/jinfinance> Dear author(s), thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points: * [ ] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/). * [ ] In the paper, please do not use country acronyms, so spell out country names. * [ ] The above code report, quoting "lines of code" counts, excludes your Nextflow .nf files. Would you be able to provide an estimate for us here in terms of lines of Nextflow code in your project? Thanks! — Reply to this email directly, view it on GitHub<#6958 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHQVONGWIII2KL4X72AXLB3ZM6DFBAVCNFSM6AAAAABKJGNY56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGA2DQNZVGY>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[jinfinance]

Thanks for letting me know, Kevin. Best, Rong From: Kevin Mattheus Moerman ***@***.***> Sent: Thursday, July 18, 2024 5:30 AM To: openjournals/joss-reviews ***@***.***> Cc: Jin, Rong (CDC/NCEZID/DFWED/EDLB) ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: Step-mothur: Nextflow-Based Quality Control and Filtering Pipeline for Highly Multiplexed Amplicon Sequencing Data (Issue #6958) CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

…

________________________________ @jinfinance<https://github.com/jinfinance> note I've just waitlisted this submission as our editors in this domain are currently busy handling other submissions. We'll assign an editor once one becomes available. — Reply to this email directly, view it on GitHub<#6958 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHQVONEBYOKS3APIQ7LIDSLZM6DINAVCNFSM6AAAAABKJGNY56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGA2TANRTGU>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[Kevin-Mattheus-Moerman]

@editorialbot invite @ppxasjsm as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@ppxasjsm this may be somewhat outside of your usual domain but I was wondering if you could help edit this one?

[Kevin-Mattheus-Moerman]

@ppxasjsm 👋 could you help edit this one?

[Kevin-Mattheus-Moerman]

@editorialbot invite @jromanowska as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@jinfinance Note I have just added the query-scope label, to trigger a scope review by the editorial board. This is because of the relatively small size of the project. During this scope review we'll determine if the functionality offered is extensive enough and if the project conforms to our substantial scholarly effort criteria. The scope review should take about 2 weeks to complete.

[jinfinance]

Hi Kevin, Thank you for initiating the scope review for our Step_mothur pipeline. Our Step_mothur pipeline addresses a critical need in HMAS(highly multiplexed amplicon sequencing) data analysis by providing automated quality control and filtering. This enables efficient outbreak detection and public health surveillance directly from stool samples, eliminating the need for isolates. Currently, 9 state public health labs (SPHL) in the United States and a collaboration with the Public Health Agency of Canada are actively using and testing our pipeline. We believe its capabilities can benefit any researchers working with HMAS data. The Step_mothur pipeline is built on the flexible Nextflow platform, allowing for easy customization and integration with downstream processes. Our team at the CIMS(Culture Independent and Metagenomic Subtyping) group at CDC has been developing and refining this pipeline for over two years. While I am currently listed as the sole lead author due to staffing changes, the pipeline has benefited from the contributions of multiple team members. We are confident that Step_mothur meets JOSS's criteria for substantial scholarly effort and offers valuable functionalities to the scientific community. Please do not hesitate to ask any questions. Sincerely, Rong Jin From: Kevin Mattheus Moerman ***@***.***> Sent: Thursday, August 8, 2024 11:56 AM To: openjournals/joss-reviews ***@***.***> Cc: Jin, Rong (CDC/NCEZID/DFWED/EDLB) ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: Step-mothur: Nextflow-Based Quality Control and Filtering Pipeline for Highly Multiplexed Amplicon Sequencing Data (Issue #6958) CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

…

________________________________ @jinfinance<https://github.com/jinfinance> Note I have just added the query-scope label, to trigger a scope review by the editorial board. This is because of the relatively small size of the project. During this scope review we'll determine if the functionality offered is extensive enough and if the project conforms to our substantial scholarly effort criteria<https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort>. The scope review should take about 2 weeks to complete. — Reply to this email directly, view it on GitHub<#6958 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHQVONHYM6BEU4JZRODGQR3ZQOIILAVCNFSM6AAAAABKJGNY56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZWGE3DGMJSGY>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[Kevin-Mattheus-Moerman]

@jinfinance Unfortunately, after review by the JOSS editorial team we've determined that this submission doesn't meet our substantial scholarly effort criterion.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

We will now proceed to reject this submission.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.