[REVIEW]: AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignmen

[editorialbot]

Submitting author: @Juke34 (Jacques Dainat)
Repository: https://github.com/Juke34/AliNe
Branch with paper.md (empty if default branch): main
Version: v1.1.1
Editor: @jromanowska
Reviewers: @rcannood, @gchure
Archive: 10.5281/zenodo.14953389

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/3691aa3dd83d8ccab8dfacce69c9b4c6/status.svg)](https://joss.theoj.org/papers/3691aa3dd83d8ccab8dfacce69c9b4c6)

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

@rcannood & @gchure, 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 @jromanowska 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 @gchure

📝 Checklist for @rcannood

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1093/BIOINFORMATICS/BTP324 is OK
- 10.1093/BIOINFORMATICS/BTP698 is OK
- 10.1038/NMETH.1923 is OK
- 10.1093/NAR/GKT214 is OK
- 10.1186/GB-2013-14-4-R36 is OK
- 10.1093/bioinformatics/bts635 is OK
- 10.1371/journal.pone.0163962 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1038/nmeth.4197 is OK
- 10.1038/nbt.3820 is OK
- 10.1371/JOURNAL.PCBI.1005944 is OK
- 10.1038/s41592-018-0001-7 is OK
- 10.1101/720458 is OK
- 10.1038/s41587-019-0201-4 is OK
- 10.1093/BIOINFORMATICS/BTAB705 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1002/imt2.107 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: novoAlign | Novocraft
- No DOI given, and none found for title: BBMap
- No DOI given, and none found for title: Aligning sequence reads, clone sequences and assem...
- No DOI given, and none found for title: FastQC

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (427.1 files/s, 70208.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         3            117              0            342
TeX                              1              0              0            285
YAML                             1              2              1             75
-------------------------------------------------------------------------------
SUM:                             5            119              1            702
-------------------------------------------------------------------------------

Commit count by author:

    46	Jacques Dainat

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 714

✅ 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 📄 👈

[jromanowska]

👋🏼 @Juke34, @rcannood, @gchure, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7545 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

I encourage you to over-communicate and let everyone know that you're on the task every now and then, instead of waiting several weeks to collect all your comments, questions, or suggestions.

Please feel free to ping me (@jromanowska) if you have any questions/concerns.

[gchure]

Review checklist for @gchure

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/Juke34/AliNe?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Juke34) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

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

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

[jromanowska]

@Juke34, @rcannood, just a reminder that you need to generate your checklists

[Juke34]

Me too? Is it not only the reviewers?

[jromanowska]

Me too? Is it not only the reviewers?

You're correct! My mistake 🙈

[gchure]

@jromanowska Just an update -- holiday travel is coming up and I may be a week or two delayed in my review. I'll keep you updated as I go through my checklist!

[rcannood]

Review checklist for @rcannood

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/Juke34/AliNe?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Juke34) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

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

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

[jromanowska]

@jromanowska Just an update -- holiday travel is coming up and I may be a week or two delayed in my review. I'll keep you updated as I go through my checklist!

No problem - we all need a break at the end of this busy year 🙏

[jromanowska]

@rcannood , @gchure - I hope you had a great end-of-the-year break.
Just sending a kind reminder about this review. Please update us on your progress as soon as you start working on it.

[rcannood]

@rcannood , @gchure - I hope you had a great end-of-the-year break. Just sending a kind reminder about this review. Please update us on your progress as soon as you start working on it.

Thanks for the reminder! I started work on reviewing the functionality and software paper.

[gchure]

@rcannood , @gchure - I hope you had a great end-of-the-year break. Just sending a kind reminder about this review. Please update us on your progress as soon as you start working on it.

Thanks for the reminder as well! My plan is to resume working on it today.

Happy New Year to everyone!

[gchure]

Hi @jromanowska, hope you're doing well! I wanted to give a quick update that I've opened some issues with #5 being the most substantive to the work. I'm having some installation issues wrt Docker on my machine that are stopping me from running the tests, but will work on that over the next few days.

[Juke34]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Done! version is now v1.1.1

[jromanowska]

@Juke34 - could you make the affiliations in Zenodo and in the paper more similar? Or please explain why are they different.

[Juke34]

Hi @jromanowska I edited the zenodo side to be similar.

[Juke34]

Should I update the release and the zenodo to integrate your last changes?

[jromanowska]

Should I update the release and the zenodo to integrate your last changes?

No, don't update the release and zenodo - these were only changes in the paper text.

[jromanowska]

@editorialbot generate pdf

[editorialbot]

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

[jromanowska]

@editorialbot generate pdf

[editorialbot]

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

[jromanowska]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.5281/zenodo.7219617 is OK
- 10.5281/zenodo.14537300 is OK
- 10.5281/zenodo.14412016 is OK
- 10.5281/zenodo.13837834 is OK
- 10.1093/BIOINFORMATICS/BTP324 is OK
- 10.1093/BIOINFORMATICS/BTP698 is OK
- 10.1186/GB-2009-10-3-R25 is OK
- 10.1038/NMETH.1923 is OK
- 10.1038/nbt.3519 is OK
- 10.1093/NAR/GKT214 is OK
- 10.1093/bioinformatics/bts635 is OK
- 10.1371/journal.pone.0163962 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1038/nmeth.4197 is OK
- 10.1038/nbt.3820 is OK
- 10.1371/JOURNAL.PCBI.1005944 is OK
- 10.1038/s41592-018-0001-7 is OK
- 10.1101/720458 is OK
- 10.1038/s41587-019-0201-4 is OK
- 10.1093/BIOINFORMATICS/BTAB705 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1002/imt2.107 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A proof of concept daisy-chaining Nextflow workflo...
- No DOI given, and none found for title: A proof of concept daisy-chaining Nextflow workflo...
- No DOI given, and none found for title: novoAlign | Novocraft
- No DOI given, and none found for title: BBMap:  A Fast, Accurate, Splice-Aware Aligner
- No DOI given, and none found for title: Aligning sequence reads, clone sequences and assem...
- No DOI given, and none found for title: FastQC

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[jromanowska]

@Juke34 - I've noticed couple of small mistakes in references:

1. "Twelve years of SAMtools and BCFtools" lacks the final author (if you compare with the webpage)
2. nf-cascade is listed as authored by you, but I can see it's done by another author
   there are two references to the same github repo (@nfcascade and @daisychainingaline) - could you check that and fix?
3. "Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM" is a manuscript title while it's formatted as journal title?
4. correct the capitalization in: "Fast and accurate short read alignment with Burrows–Wheeler transform", "The subreadr aligner:", "SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation"
5. "Salmon provides fast and bias-aware quantification of transcript expression" and "Accurate detection of complex structural variations using single-molecule sequencing" - the journal title should say only "Nature Methods"

Please, correct and re-generate the pdf here.

[Juke34]

Thank you for your carefull review

@Juke34 - I've noticed couple of small mistakes in references:

1. "Twelve years of SAMtools and BCFtools" lacks the final author (if you compare with the webpage)

What a shame to have forgotten Heng Li, thank you for pointing it is fixed now.

2. nf-cascade is listed as authored by you, but I can see it's done by another author
   there are two references to the same github repo (@nfcascade and @daisychainingaline) - could you check that and fix?

I fixed the mistake.

3. "Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM" is a manuscript title while it's formatted as journal title?

I'm not sure to understand why you say it is formatted as journal title... is it due to BWA-MEM in capital? It is just kept as provided [here]("Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM" is a manuscript title while it's formatted as journal title?) or here.
Let me know what you expect (lower case "BWA-MEM"?).

4. correct the capitalization in: "Fast and accurate short read alignment with Burrows–Wheeler transform", "The subreadr aligner:", "SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation"

I do not see any rule from JOSS saying we need to capitalize title, I thought we must stick to the original capitalisation where it was published. In that light, I updated only the last one (SeqKit). Let me know if I really have to capitalize the two others.

5. "Salmon provides fast and bias-aware quantification of transcript expression" and "Accurate detection of complex structural variations using single-molecule sequencing" - the journal title should say only "Nature Methods">

Good catch, it is fixed now.

Please, correct and re-generate the pdf here.

[Juke34]

@editorialbot generate pdf

[editorialbot]

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

[jromanowska]

Thanks for quick fixes!

What I meant in pt.4 above is that the "Burrows-Wheeler" and "FASTA/Q" are written as "burrows-wheeler" and "FASTA/q" in your reference list.

Ad.point 3 - I ment that there is no journal title and the article title is in italics, as if it was journal title. I can see in the .bib file that you've formatted this citation from arxiv as "misc" while another one, from biorxiv is correctly formatted as "article". If you change the format to "article", it will look nicer.

[Juke34]

Thanks for quick fixes!

What I meant in pt.4 above is that the "Burrows-Wheeler" and "FASTA/Q" are written as "burrows-wheeler" and "FASTA/q" in your reference list.

For that point I don't know what I should do. The JOSS reference processing put everything in lower case except first character in the title and any word that is in CAPITAL it is whole. So DNA stay DNA but "Burrows-Wheeler" becomes "burrows-wheeler". / is seen as non-word character and "FASTA/Q" becomes "FASTA/q".

Ad.point 3 - I ment that there is no journal title and the article title is in italics, as if it was journal title. I can see in the .bib file that you've formatted this citation from arxiv as "misc" while another one, from biorxiv is correctly formatted as "article". If you change the format to "article", it will look nicer.

This is fixed now

[Juke34]

@editorialbot generate pdf

[editorialbot]

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

[jromanowska]

Oh, it's the bibtex-way: you put the entire title in extra pair of curly braces :) I've made a pull request for you.

[Juke34]

Thx I didn't know it was possible to do like that.

[Juke34]

@editorialbot generate pdf

[editorialbot]

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

[jromanowska]

Thank you, again, @Juke34, @rcannood, @gchure - the editor-in-chief will now perform last checks and prepare everything for publication! :)

[jromanowska]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.5281/zenodo.7219617 is OK
- 10.5281/zenodo.14537300 is OK
- 10.5281/zenodo.14412016 is OK
- 10.5281/zenodo.13837834 is OK
- 10.1093/BIOINFORMATICS/BTP324 is OK
- 10.1093/BIOINFORMATICS/BTP698 is OK
- 10.1186/GB-2009-10-3-R25 is OK
- 10.1038/NMETH.1923 is OK
- 10.1038/nbt.3519 is OK
- 10.1093/NAR/GKT214 is OK
- 10.1093/bioinformatics/bts635 is OK
- 10.1371/journal.pone.0163962 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1038/nmeth.4197 is OK
- 10.1038/nbt.3820 is OK
- 10.1371/JOURNAL.PCBI.1005944 is OK
- 10.1038/s41592-018-0001-7 is OK
- 10.1101/720458 is OK
- 10.1038/s41587-019-0201-4 is OK
- 10.1093/BIOINFORMATICS/BTAB705 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1002/imt2.107 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A proof of concept daisy-chaining Nextflow workflo...
- No DOI given, and none found for title: Daisy chaining AliNe
- No DOI given, and none found for title: novoAlign | Novocraft
- No DOI given, and none found for title: BBMap:  A Fast, Accurate, Splice-Aware Aligner
- No DOI given, and none found for title: Aligning sequence reads, clone sequences and assem...
- No DOI given, and none found for title: FastQC

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6475, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept