[PRE REVIEW]: Viash: A meta-framework for building reusable workflow modules

[editorialbot]

Submitting author: !--author-handle-->@rcannood<!--end-author-handle-- (Robrecht Cannoodt) Repository: https://github.com/viash-io/viash Branch with paper.md (empty if default branch): paper Version: 0.8.1 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @wilkinson, @abhishektiwari, @mberacochea Managing EiC: Daniel S. Katz

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

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (492.3 files/s, 30686.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             48              0             85
TeX                              1             11              0             43
-------------------------------------------------------------------------------
SUM:                             3             59              0            128
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1876

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/bts480 is OK
- 10.1038/s41592-019-0654-x is OK
- 10.1038/s41576-023-00586-w is OK
- 10.15252/msb.20188746 is OK
- 10.1038/s41587-020-0439-x is OK
- 10.1038/nbt.3820 is OK
- 10.5281/ZENODO.4638196 is OK
- 10.5281/ZENODO.4735634 is OK
- 10.1371/journal.pone.0177459 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis Submitting author: @ParkvilleData Handling editor: @jmschrei (Active) Reviewers: @Ebedthan, @rjorton Similarity score: 0.8208

BioProv - A provenance library for bioinformatics workflows Submitting author: @vinisalazar Handling editor: @jmschrei (Active) Reviewers: @maximtrp, @Zethson Similarity score: 0.8190

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: 0.8181

DARE Platform: a Developer-Friendly and Self-Optimising Workflows-as-a-Service Framework for e-Science on the Cloud Submitting author: @iaklampanos Handling editor: @danielskatz (Active) Reviewers: @rafaelfsilva, @Himscipy Similarity score: 0.8180

⚠️ 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.

[danielskatz]

👋 @rcannood - JOSS works best when the paper branch contains the software as well, not just the paper. Can you please change the paper branch of be a copy of main that also includes the paper, rather than just the paper?

[danielskatz]

Also, your figures are not appearing in the draft paper. Please follow the example paper. Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[rcannood]

Thanks @danielskatz ! I'll make some changes to make the paper render properly. It's strange because when I rendered the paper locally using docker run ... openjournals/inara, everything looks ok.

[rcannood]

@editorialbot generate pdf

[rcannood]

@editorialbot commands

[editorialbot]

Hello @rcannood, here are the things you can ask me to do:

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[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:

nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline Submitting author: @ZeyuanSong Handling editor: @lpantano (Active) Reviewers: @preetida, @rspirgel Similarity score: 0.8333

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis Submitting author: @ParkvilleData Handling editor: @jmschrei (Active) Reviewers: @Ebedthan, @rjorton Similarity score: 0.8208

BioProv - A provenance library for bioinformatics workflows Submitting author: @vinisalazar Handling editor: @jmschrei (Active) Reviewers: @maximtrp, @Zethson Similarity score: 0.8190

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: 0.8181

DARE Platform: a Developer-Friendly and Self-Optimising Workflows-as-a-Service Framework for e-Science on the Cloud Submitting author: @iaklampanos Handling editor: @danielskatz (Active) Reviewers: @rafaelfsilva, @Himscipy Similarity score: 0.8180

⚠️ 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.

[rcannood]

@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:

nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline Submitting author: @ZeyuanSong Handling editor: @lpantano (Active) Reviewers: @preetida, @rspirgel Similarity score: 0.8280

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis Submitting author: @ParkvilleData Handling editor: @jmschrei (Active) Reviewers: @Ebedthan, @rjorton Similarity score: 0.8197

Pipengine: an ultra light YAML-based pipeline execution engine Submitting author: @fstrozzi Handling editor: @biorelated (Retired) Reviewers: @yannickwurm Similarity score: 0.8173

BioProv - A provenance library for bioinformatics workflows Submitting author: @vinisalazar Handling editor: @jmschrei (Active) Reviewers: @maximtrp, @Zethson Similarity score: 0.8121

SIAL: A simple image analysis library for wet-lab scientists Submitting author: @d-tear Handling editor: @jni (Retired) Reviewers: @bogovicj, @haesleinhuepf Similarity score: 0.8110

⚠️ 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.

[rcannood]

@danielskatz Looks like all the figures are there now :)

[rcannood]

@danielskatz Here is a potential list of reviewers:

• mberacochea - Previously reviewed Baargin: a Nextflow workflow ... and ALPPACA together with me. Has a lot of activity related to Nextflow workflows and modules in his GitHub Contribution activity.
• hseabolt - Also reviewed ALPPACA together with me, and has activity related to Nextflow workflows and modules in his GitHub Contribution activity.
• Zethson - Previously reviewed BioProv - A provenance library for bioinformatics workflows, and also has activity related to Nextflow workflows in his GitHub Contribution activity

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.29 s (1058.7 files/s, 151056.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Scala                          195           3439           3538          18353
SVG                              4              0              0          11803
Markdown                         7           1033              0           2310
YAML                            44             33             19           1444
Bourne Shell                    46            273            219           1392
Python                           8             52             19            144
JavaScript                       1              9              4             65
TeX                              1             11              0             43
R                                1              8             14             40
JSON                             1              1              0             20
Dockerfile                       1              6              7             18
EJS                              1              0              0              9
Rmd                              1              9             40              0
-------------------------------------------------------------------------------
SUM:                           311           4874           3860          35641
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1872

[danielskatz]

@rcannood - thanks for your changes. I'll assign myself as the editor and get started on looking for reviewers.

As a note, this paper is fairly long now (JOSS recommends 1000 words as a maximum), so if you add anything during the review process, please find something else to remove at the same time.

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[danielskatz]

👋 @mberacochea, @hseabolt, @Zethson - would any of you be willing to review this JOSS submission?

[hseabolt]

Unfortunately I'm not currently available for this review, sorry!

[danielskatz]

@editorialbot add @wilkinson as reviewer

(Thanks for volunteering to help on this)

[editorialbot]

@wilkinson added to the reviewers list!

[abhishektiwari]

@danielskatz I am open to review workflow related submissions. Feel free to assign me as additional reviewer on this. Seems like an intersting approach to build modular data pipelines.

[danielskatz]

thanks @abhishektiwari - I'll add you, but I'm going to try to find one more reviewer before we start

[danielskatz]

@editorialbot add @abhishektiwari as reviewer

[editorialbot]

@abhishektiwari added to the reviewers list!

[Zethson]

I'll have to politely decline. Currently swamped.

[mberacochea]

Hi all. I can review this one, happy to do so as I'm interested in that tool :).

[danielskatz]

Thanks @mberacochea - I'll add you, and we'll start the review

[danielskatz]

@editorialbot add @mberacochea as reviewer

[editorialbot]

@mberacochea added to the reviewers list!

[danielskatz]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6089.

[rcannood]

@danielskatz @warrickball @abhishektiwari @mberacochea Thank you all for agreeing to review this paper. I look forward to your feedback!