[PRE REVIEW]: AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignmen #7348

editorialbot · 2024-10-14T10:19:13Z

Submitting author: @Juke34 (Jacques Dainat)
Repository: https://github.com/Juke34/AliNe
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @jromanowska
Reviewers: @rcannood, @gchure
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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

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editorialbot · 2024-10-14T10:19:16Z

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2024-10-14T10:19:39Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (345.6 files/s, 62208.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             76              0            294
TeX                              1              0              0            272
YAML                             1              2              1             75
-------------------------------------------------------------------------------
SUM:                             4             78              1            641
-------------------------------------------------------------------------------

Commit count by author:

    41	Jacques Dainat

editorialbot · 2024-10-14T10:19:42Z

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
- 10.1093/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
- 10.1093/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
- No DOI given, and none found for title: A Recent ( 2020 ) Comparative Analysis of Genome A...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.1186/GB-2013-14-4-R36/FIGURES/6 is INVALID

editorialbot · 2024-10-14T10:19:46Z

Paper file info:

📄 Wordcount for paper.md is 712

🔴 Failed to discover a Statement of need section in paper

editorialbot · 2024-10-14T10:19:48Z

License info:

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

editorialbot · 2024-10-14T10:20:51Z

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

editorialbot · 2024-10-14T10:21:37Z

Five most similar historical JOSS papers:

sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files
Submitting author: @maxibor
Handling editor: @jmschrei (Active)
Reviewers: @fasnicar, @marouenbg
Similarity score: 0.7372

RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease
Submitting author: @serine
Handling editor: @pjotrp (Retired)
Reviewers: @andrewyatz
Similarity score: 0.7187

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: 0.7062

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
Submitting author: @hkaspersen
Handling editor: @csoneson (Active)
Reviewers: @mberacochea, @hseabolt, @rcannood
Similarity score: 0.7055

A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments
Submitting author: @mgalland
Handling editor: @brainstorm (Retired)
Reviewers: @vladsaveliev
Similarity score: 0.6999

⚠️ 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 · 2024-10-20T13:49:45Z

@Juke34 Dear author, 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:

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
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/).
Since cloc does not count lines of nextflow code, could you help provide a summary of the number of lines of code contained in this submission (that are fully your own work). Thanks!
Please format the paper as per our guidelines, i.e. a Statement of Need section is needed. You can call @editorialbot generate pdf here to update the paper.

Juke34 · 2024-10-21T19:14:49Z

@editorialbot check reference

editorialbot · 2024-10-21T19:14:51Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Juke34 · 2024-10-21T19:15:38Z

@editorialbot check references

editorialbot · 2024-10-21T19:15:56Z

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
- 10.1093/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
- No DOI given, and none found for title: A Recent ( 2020 ) Comparative Analysis of Genome A...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

Juke34 · 2024-10-21T19:26:31Z

@editorialbot check references

editorialbot · 2024-10-21T19:26:50Z

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

Juke34 · 2024-10-21T19:28:52Z

@editorialbot generate pdf

editorialbot · 2024-10-21T19:30:35Z

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

editorialbot · 2024-10-21T19:31:22Z

Five most similar historical JOSS papers:

sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files
Submitting author: @maxibor
Handling editor: @jmschrei (Active)
Reviewers: @fasnicar, @marouenbg
Similarity score: 0.7475

RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease
Submitting author: @serine
Handling editor: @pjotrp (Retired)
Reviewers: @andrewyatz
Similarity score: 0.7246

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: 0.7173

A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments
Submitting author: @mgalland
Handling editor: @brainstorm (Retired)
Reviewers: @vladsaveliev
Similarity score: 0.7018

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
Submitting author: @hkaspersen
Handling editor: @csoneson (Active)
Reviewers: @mberacochea, @hseabolt, @rcannood
Similarity score: 0.6958

⚠️ 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.

Juke34 · 2024-10-21T19:36:42Z

Dear @Kevin-Mattheus-Moerman,

I have addressed all the issues you pointed out.
About the number of lines of code contained in this submission, it should be 3538 lines (counted using wc -l)

Best regards,

Jacques Dainat

Kevin-Mattheus-Moerman · 2024-11-01T15:34:17Z

@editorialbot invite @jromanowska as editor

editorialbot · 2024-11-01T15:34:20Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2024-11-01T15:34:39Z

@jromanowska do you think you can help edit this one?

jromanowska · 2024-11-03T11:49:56Z

Sure!

jromanowska · 2024-11-03T11:50:06Z

@editorialbot assign me as editor

editorialbot · 2024-11-03T11:50:09Z

Assigned! @jromanowska is now the editor

jromanowska · 2024-11-03T11:50:50Z

Hi, @Juke34 👋
I will take care of the process from now on. I will try to find reviewers, but please let me know if you have any suggestions (or oppositions). When naming reviewers, write their GitHub handles without @, so that they won't get notified.

Juke34 · 2024-11-04T13:37:04Z

Hi @jromanowska, here a list of potential reviewers:

stevokeyo
rcannood
adrientaudiere
gchure

jromanowska · 2024-11-11T08:20:51Z

👋 @hkaspersen, @jhayer, @stevokeyo, @rcannood, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

jhayer · 2024-11-12T10:49:24Z

Hi, I am sorry but I will have to decline for this review. We have a conflict of interest here.
Kind regards,
Juliette

jromanowska · 2024-11-12T11:06:34Z

Hi, I am sorry but I will have to decline for this review. We have a conflict of interest here. Kind regards, Juliette

Thank you for the reply, @jhayer. Could you suggest someone who might be able to review this software? (Preferentially not a cis-male)

rcannood · 2024-11-12T20:24:27Z

I can review!

I am a cis male, though, so not sure whether I'm still eligible 😅

jromanowska · 2024-11-13T07:31:09Z

I can review!

I am a cis male, though, so not sure whether I'm still eligible 😅

Thanks, @rcannood! Yes, you are eligible. ;) I was asking Juliette for recommendations for someone non cis-male because all the other people I could find were (assumingly) cis-male. It's always good to have a broad spectrum of reviewers, if possible.

hkaspersen · 2024-11-16T10:23:28Z

@jromanowska I am sorry I am unable to provide a review here, currently swamped! But thank you for the invitation!

jromanowska · 2024-11-18T08:17:20Z

@jromanowska I am sorry I am unable to provide a review here, currently swamped! But thank you for the invitation!

That's fine, thanks for letting us know. If you know anyone who could be willing to review this, write their emails or GitHub handles here (but without the '@' sign).

jromanowska · 2024-11-18T08:17:34Z

@editorialbot add @rcannood as reviewer

editorialbot · 2024-11-18T08:17:36Z

@rcannood added to the reviewers list!

jromanowska · 2024-12-02T08:20:56Z

👋 @adrientaudiere, @gchure, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

gchure · 2024-12-02T17:11:38Z

Hi @jromanowska, happy to review!

jromanowska · 2024-12-02T17:58:42Z

@editorialbot add @gchure as reviewer

editorialbot · 2024-12-02T17:58:44Z

@gchure added to the reviewers list!

jromanowska · 2024-12-02T17:59:15Z

@editorialbot start review

editorialbot · 2024-12-02T17:59:19Z

OK, I've started the review over in #7545.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Oct 14, 2024

editorialbot added Nextflow TeX labels Oct 14, 2024

editorialbot assigned jromanowska Nov 3, 2024

editorialbot assigned rcannood Nov 18, 2024

editorialbot assigned gchure Dec 2, 2024

editorialbot closed this as completed Dec 2, 2024

[PRE REVIEW]: AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignmen #7348

[PRE REVIEW]: AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignmen #7348

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