search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
720 stars 38 forks source link

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

Open editorialbot opened 2 weeks ago

editorialbot commented 2 weeks ago

Submitting author: !--author-handle-->@Juke34<!--end-author-handle-- (Jacques Dainat) Repository: https://github.com/Juke34/AliNe Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3691aa3dd83d8ccab8dfacce69c9b4c6"><img src="https://joss.theoj.org/papers/3691aa3dd83d8ccab8dfacce69c9b4c6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3691aa3dd83d8ccab8dfacce69c9b4c6/status.svg)](https://joss.theoj.org/papers/3691aa3dd83d8ccab8dfacce69c9b4c6)

Author instructions

Thanks for submitting your paper to JOSS @Juke34. Currently, there isn't a JOSS editor assigned to your paper.

@Juke34 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 commented 2 weeks ago

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:

@editorialbot generate pdf
editorialbot commented 2 weeks ago

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 commented 2 weeks ago 
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 commented 2 weeks ago

Paper file info:

📄 Wordcount for paper.md is 712

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 2 weeks ago

License info:

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

editorialbot commented 2 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 2 weeks ago

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 commented 1 week ago

@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:

Juke34 commented 6 days ago

@editorialbot check reference

editorialbot commented 6 days ago

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

@editorialbot commands

Juke34 commented 6 days ago

@editorialbot check references

editorialbot commented 6 days ago 
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 commented 6 days ago

@editorialbot check references

editorialbot commented 6 days ago 
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 commented 6 days ago

@editorialbot generate pdf

editorialbot commented 6 days ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 6 days ago

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 commented 6 days ago

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