[PRE REVIEW]: Acanthophis: a comprehensive plant hologenomics pipeline

[editorialbot]

Submitting author: @kdm9 (Kevin Murray)
Repository: https://github.com/kdm9/Acanthophis
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @marcosvital
Reviewers: @bricoletc, @gbouras13, @abhishektiwari
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366"><img src="https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366/status.svg)](https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366)

Author instructions

Thanks for submitting your paper to JOSS @kdm9. Currently, there isn't a JOSS editor assigned to your paper.

@kdm9 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]

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:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (2080.0 files/s, 102314.6 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
YAML                             35             64            192            897
Markdown                          7            171              0            600
TeX                               1             27              0            464
Python                            7             71             58            303
Bourne Again Shell                4             23             26            113
Bourne Shell                      7              9             16             48
TOML                              1              1              0             11
Dockerfile                        1              1              0              4
--------------------------------------------------------------------------------
SUM:                             63            367            292           2440
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1101/2021.08.07.455511 is OK
- 10.21105/joss.05627 is OK
- 10.1038/nmeth.3176 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.48550/arXiv.2309.15884 is OK
- 10.1101/2022.04.08.487684 is OK
- 10.1101/gr.210641.116 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.5281/ZENODO.4677629 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/bioinformatics/btr509 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btab705 is OK
- 10.1186/1756-0500-5-337 is OK
- 10.7717/peerj-cs.104 is OK
- 10.1038/ncomms11257 is OK
- 10.1371/journal.pbio.1002311 is OK
- 10.1371/journal.pcbi.1005727 is OK
- 10.1111/mec.15287 is OK
- 10.1186/s13059-016-0997-x is OK
- 10.1038/s41396-020-0665-8 is OK
- 10.1186/s13104-016-1900-2 is OK
- 10.1093/bioinformatics/btt468 is OK
- 10.6084/m9.figshare.13174337.v1 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.5281/ZENODO.7728364 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 932

[kdm9]

FYI: cloc doesn't count the actual code of Acanthophis, which is in snakemake *.rules files:

$ wc -l acanthophis/template/workflow/Snakefile acanthophis/template/workflow/rules/*.rules
   33 acanthophis/template/workflow/Snakefile
  347 acanthophis/template/workflow/rules/align.rules
  331 acanthophis/template/workflow/rules/base.rules
  121 acanthophis/template/workflow/rules/denovo.rules
  315 acanthophis/template/workflow/rules/metagenome.rules
  339 acanthophis/template/workflow/rules/reads.rules
  207 acanthophis/template/workflow/rules/sampleset.rules
  278 acanthophis/template/workflow/rules/taxonid.rules
  408 acanthophis/template/workflow/rules/varcall.rules
   46 acanthophis/template/workflow/rules/variantannotation.rules
 2425 total

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[kdm9]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis
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Handling editor: @mgymrek (Retired)
Reviewers: @luizirber
Similarity score: 0.8223

⚠️ 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 before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@editorialbot invite @marcosvital as editor

[editorialbot]

Invitation to edit this submission sent!

[marcosvital]

@editorialbot assign @marcosvital as editor

[editorialbot]

Assigned! @marcosvital is now the editor

[marcosvital]

Hi, @kdm9, I will be the editor of your submission.

Please take a look at the manuscript proof you generated above, and check if it seems ok and ready to review. If you make any changes or corrections on it you can create a new version anytime. I saw a small type: Stage 6 is written as Stage 5.

At the same time, we can start assigning reviewers for you submission. We usually ask the authors for suggestions, so let me know if you have anyone in mind that could do this - you can paste the github profile of anyone you think that could do it (but please don't tag anyone yet).
You can also check and search using this list of people that have agreed to review for JOSS, and see if any of them may be suitable to review this submission.

[kdm9]

Hi @marcosvital , thanks for editing!

I have fixed those and a few extra minor grammar/citation issues, and hopefully now after a

@editorialbot generate pdf

the PDF should be in a final draft state and ready to review.

Regarding reviewers, from that list I would suggest the following, if they have time:

• https://github.com/aboffin
• https://github.com/gbouras13
• https://github.com/bricoletc
• https://github.com/standage
• https://github.com/camillescott
• https://github.com/conradstack

(though I note a bit of a lack of plant genomics/informatics folks in JOSS -- I need to do some spruiking of JOSS in these circles it seems!!)

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
Submitting author: @hkaspersen
Handling editor: @csoneson (Active)
Reviewers: @mberacochea, @hseabolt, @rcannood
Similarity score: 0.8396

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis
Submitting author: @ParkvilleData
Handling editor: @jmschrei (Active)
Reviewers: @Ebedthan, @rjorton
Similarity score: 0.8336

Phylen: automatic phylogenetic reconstruction using the EggNOG database
Submitting author: @giraola
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @juanvillada
Similarity score: 0.8271

Corekaburra: pan-genome post-processing using core gene synteny
Submitting author: @milnus
Handling editor: @csoneson (Active)
Reviewers: @iferres, @asafpr
Similarity score: 0.8239

chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data
Submitting author: @greatfireball
Handling editor: @pjotrp (Retired)
Reviewers: @jdeligt
Similarity score: 0.8198

⚠️ 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 before considering asking the reviewers of these papers to review again for JOSS.

[kdm9]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
Submitting author: @akrinos
Handling editor: @will-rowe (Retired)
Reviewers: @johanneswerner, @jcmcnch
Similarity score: 0.8384

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis
Submitting author: @ParkvilleData
Handling editor: @jmschrei (Active)
Reviewers: @Ebedthan, @rjorton
Similarity score: 0.8296

Phylen: automatic phylogenetic reconstruction using the EggNOG database
Submitting author: @giraola
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @juanvillada
Similarity score: 0.8247

Corekaburra: pan-genome post-processing using core gene synteny
Submitting author: @milnus
Handling editor: @csoneson (Active)
Reviewers: @iferres, @asafpr
Similarity score: 0.8191

phyphy: Python package for facilitating the execution and parsing of HyPhy standard analyses
Submitting author: @sjspielman
Handling editor: @mgymrek (Retired)
Reviewers: @luizirber
Similarity score: 0.8178

⚠️ 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 before considering asking the reviewers of these papers to review again for JOSS.

[marcosvital]

Dear @aboffin, @gbouras13 and @bricoletc, would you be willing to review this submission for JOSS?

We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission.

[gbouras13]

@marcosvital I'm happy to review this

[bricoletc]

@marcosvital @kdm9, yes, happily!

[gbouras13]

@editorialbot generate my checklist

[editorialbot]

Checklists can only be created once the review has started in the review issue

[gbouras13]

Hi @marcosvital,

Just letting you know this is my first JOSS review - so please just prod me to do things if required.

George

[gbouras13]

sorry I just tried this as someone did it on my paper being reviewed at the moment - apologies.

[marcosvital]

sorry I just tried this as someone did it on my paper being reviewed at the moment - apologies.

No problem at all, this command will work once we start the review (which will happen in a different GitHub issue).

[marcosvital]

Thank you @gbouras13 and @bricoletc, we will start the review soon.

[marcosvital]

@editorialbot add @bricoletc as reviewer

[editorialbot]

@bricoletc added to the reviewers list!

[marcosvital]

@editorialbot add @gbouras13 as reviewer

[editorialbot]

@gbouras13 added to the reviewers list!

[marcosvital]

Dear @standage, would you be willing to review this submission for JOSS?

We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission.

[standage]

Thank you for the invite @marcosvital, but I'm going to have to decline this time.

[aboffin]

@marcosvital<https://github.com/marcosvital> Thank you for the invite, unfortunately I am unable to review this submission at this moment. From: Marcos Vital (LEQ-UFAL) ***@***.***> Date: Thursday, October 26, 2023 at 9:02 AM To: openjournals/joss-reviews ***@***.***> Cc: Senthil Murugapiran ***@***.***>, Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: Acanthophis: a comprehensive plant hologenomics pipeline (Issue #5953) 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. Dear @aboffin<https://github.com/aboffin>, @gbouras13<https://github.com/gbouras13> and @bricoletc<https://github.com/bricoletc>, would you be willing to review this submission for JOSS? We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission. — Reply to this email directly, view it on GitHub<#5953 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAJFEHGAILN35LRWA6JGT63YBJUOFAVCNFSM6AAAAAA6A2FSWKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBRGE4TIOBVG4>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[marcosvital]

Thank you for letting me know, @aboffin and @standage.

[marcosvital]

Dear @camillescott, would you be willing to review this submission for JOSS?

We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission.

[abhishektiwari]

@marcosvital I have used Snakemake pipelines, so open to review this paper. Feel free to assign me as a reviewer.

[marcosvital]

Thank you, @abhishektiwari

[marcosvital]

@editorialbot add @abhishektiwari as reviewer

[editorialbot]

@abhishektiwari added to the reviewers list!

[marcosvital]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6062.