[PRE REVIEW]: Fasten with Pipes

[editorialbot]

Submitting author: !--author-handle-->@lskatz<!--end-author-handle-- (Lee Katz) Repository: https://github.com/lskatz/fasten Branch with paper.md (empty if default branch): Version: v0.7.2 Editor: !--editor-->@kellyrowland<!--end-editor-- Reviewers: @telatin, @bovee Managing EiC: Kevin M. Moerman

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=4.34 s (2861.6 files/s, 112808.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                         12087          18990              0         463736
Rust                            25            573           1200           2589
JavaScript                     263              0              2           1210
Bourne Shell                    31            228             63            720
Markdown                         4             78              0            239
YAML                             4             18             17            152
TOML                             1             22              3             86
TeX                              1              4              0             37
SVG                              7              0              0             30
Dockerfile                       1              9              1             28
CSS                              7              0              1              7
-------------------------------------------------------------------------------
SUM:                         12431          19922           1287         468834
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1371/journal.pone.0163962 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 535

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

Nanoq: ultra-fast quality control for nanopore reads Submitting author: @esteinig Handling editor: @luizirber (Active) Reviewers: @natir, @bovee Similarity score: 0.8302

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: 0.8274

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences Submitting author: @warrenlr Handling editor: @biorelated (Retired) Reviewers: @andrewjpage Similarity score: 0.8273

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis Submitting author: @ParkvilleData Handling editor: @jmschrei (Active) Reviewers: @Ebedthan, @rjorton Similarity score: 0.8261

SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data Submitting author: @lskatz Handling editor: @lpantano (Active) Reviewers: @lfaller, @erinyoung, @druvus Similarity score: 0.8138

⚠️ 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]

@lskatz thanks for this submission. I am the AEiC for this track, and here to help process the initial steps. For the moment please address the below in order for your submission to be considered for JOSS:

• [x] In your affiliations, please spell out USA as United States of America.
• [x] The images (and therefore the font) in figure 1 are rather small. Please increase these, it seems feasible given that there is a lot of white space between them too.
• [x] Your paper is not formatted according to our guidelines (and lacks the require "statement of need" section too). Please have a look here, https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain, and rewrite/reorganise your paper accordingly.
• [x] I recommend that you extend your paper title as is usual for JOSS, e.g. some like the format <project name>: <A sentence on what the software does>
• [x] The following sentence (the first one in the paper) seems a bit unclear to me (perhaps it is just me): There are still many gaps in basic command line bioinformatics for standard file formats., do you mean something like: There are still many gaps in basic command line tools for bioinformatics for handling of standard file formats.?

[lskatz]

Thank you for helping me on these points. For the resolution of the figure, would it help to separate it into 9 figures? When I combine them into a single image, I think my program is compressing the resolution. Or would having 9 figures make the manuscript too verbose?

[Kevin-Mattheus-Moerman]

@lskatz I think a single merged figure is best. It may work if you simply have them nearly touching, so to remove the white space between them, and to then use the full page width. You also should be able to turn of compression for the software you are using. Anyway, give it a go and we'll look when you have the new draft.

[lskatz]

@Kevin-Mattheus-Moerman This looks much better with your suggestions. I have addressed all five of your points hopefully to your approval.

[lskatz]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences Submitting author: @warrenlr Handling editor: @biorelated (Retired) Reviewers: @andrewjpage Similarity score: 0.8148

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: 0.8130

Finch: a tool adding dynamic abundance filtering to genomic MinHashing Submitting author: @bovee Handling editor: @biorelated (Retired) Reviewers: @HadrienG Similarity score: 0.8073

SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data Submitting author: @lskatz Handling editor: @lpantano (Active) Reviewers: @lfaller, @erinyoung, @druvus Similarity score: 0.8040

fqfa: A pure Python package for genomic sequence files Submitting author: @afrubin Handling editor: @lpantano (Active) Reviewers: @natir, @FlorianThibord Similarity score: 0.8029

⚠️ 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]

@lskatz this looks better indeed. Below is some more feedback for you before we proceed.

• [ ] Although the paper now contains the required sections. I do think it would be better to rename the Materials section, for instance to Implementation. If there is any more implementation detail that you could add, that would not be doubling the documentation too much, then I would consider fleshing this section out a bit.
• [ ] In addition the Results section could perhaps be renamed for instance to something like Documentation, testing, and benchmarking. Next you can provide a little more detail on these aspects. For instance add some basic information on testing, e.g. what the tests cover, and what automated testing approaches are included. The benchmarking is interesting. Currently however, the reader has no idea what those images are about. So there is almost not point to have the image in the paper at the moment. It would be good to briefly explain the nature of the benchmarking, i.e. enough so that readers understand the nature of those graphs and the "performance" enhancements you claim/present.
• [ ] Finally I would ask that you include a CONTRIBUTING.md file in your main repository folder, which contains required contributing guidelines. Next I would recommend adding a "How to contribute to Fasten" section in the README, and to link to the CONTRIBUTING.md file there. Here are some examples of such files: https://contributing.md/example/. If you feel a dedicated file is a bit overkill for your project, you could instead simply have a longer section on this (detailing how you'd like folks to contribute to your project) in your README.

I will start looking for a handling editor but please consider the above.

[Kevin-Mattheus-Moerman]

@editorialbot invite @kellyrowland as editor

[editorialbot]

Invitation to edit this submission sent!

[lskatz]

Thank you! Your comments have made the manuscript better. I updated the manuscript's headers, and added onto the testing/benchmarking/documentation section, and added in the markdown files to guide in contributions.

Separately, I have separately asked @telatin if he would like to review this paper and he seems interested, and so I would like to put him forward as a possible reviewer.

[lskatz]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences Submitting author: @warrenlr Handling editor: @biorelated (Retired) Reviewers: @andrewjpage Similarity score: 0.8111

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: 0.8097

Finch: a tool adding dynamic abundance filtering to genomic MinHashing Submitting author: @bovee Handling editor: @biorelated (Retired) Reviewers: @HadrienG Similarity score: 0.8077

CheckQC: Quick quality control of Illumina sequencing runs Submitting author: @johandahlberg Handling editor: @pjotrp (Retired) Reviewers: @brainstorm Similarity score: 0.8000

SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data Submitting author: @lskatz Handling editor: @lpantano (Active) Reviewers: @lfaller, @erinyoung, @druvus Similarity score: 0.8000

⚠️ 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.

[lskatz]

I think some potential reviewers could include

• telatin
• audy
• luizirber
• bovee
• boydgreenfield

Not all of them are on the list of self-volunteering reviewers however.

[kellyrowland]

I can take this on, sure. @lskatz thanks for the list of reviewers; I'll ping a few folks once I'm assigned as editor.

[Kevin-Mattheus-Moerman]

@editorialbot assign @kellyrowland as editor

[editorialbot]

Assigned! @kellyrowland is now the editor

[kellyrowland]

hi @telatin @bovee 👋 would you be interested and available for reviewing this JOSS submission?

[telatin]

Sure :)

[kellyrowland]

@editorialbot add @telatin as reviewer

[editorialbot]

@telatin added to the reviewers list!

[kellyrowland]

thanks @telatin ! once we have a second reviewer lined up I'll start the review.

[bovee]

Hi, I'd be happy to review.

[kellyrowland]

great, thanks!

[kellyrowland]

@editorialbot add @bovee as reviewer

[editorialbot]

@bovee added to the reviewers list!

[kellyrowland]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6030.