PONE-D-23-11089Scikick: a sidekick for workflow clarity and reproducibility during extensive data analysisPLOS ONE

Dear Dr. Oh,

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Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

Dear authors the paper contributes an important work. Please carefully revise the manuscript addressing the comments of Rev. 1 and 2. Provide a revised manuscript with changes/additions highlighted in different color.

We will be glad to review your revised manuscript once the points have been addressed.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: N/A

Reviewer #3: N/A

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In this work, authors present Scikick, an interesting tool to create workflows composed by notebooks rather than from scripts or executable files as we all are used to do.

I have never heard about a similar tool and many times wondered how that could be done, so my overall opinion is that this is a good addition to the bioinformatics software ecosystem.

Authors have made a great effort to automatically run notebooks using Snakemake and provide exhaustive documentation to get started with the tool, including basic and advanced usage examples.

Regarding the paper, I have struggled a little bit with figure 2. I was able to fully understand it after browsing the example report online and navigating trough the different sections, so my suggestion is try improving the figure 2 legend so that readers can understand it easier. For instance, you could add a files tree of the project and briefly explain them.

In addition, three points:

- I'd suggest authors adding a new section (and maybe a figure) to explain the basic commands of the "sk" tool (init, add, status and run) as it is important for readers to see how the tool works and how dependencies are defined.

- Have you considered including tools or some mechanisms to obtain user-friendly readable diffs between notebook files? By default, "git diff" commands on Python notebooks are not very useful.

- Regarding figure 3, what does mean "verified archive"? I think that this figure can be also improved. For me, the flow would go from local development to the GitLab server and from that point the execution of the "continuous analysis" triggered. With the current image, one can think that the continuous analysis is performed in the same computer as the workflow is being developed.

Reviewer #2: The authors describe a command-line software package for tracking the sequence in which Jupyter notebooks are executed and "to define dependence between notebooks and to manage each notebook’s state." The goal is to prevent scientists from having to perform these tasks manually, which can be time consuming and error prone. For scientists who use notebooks, this tool may be helpful. Though in my own personal case, I have not yet found a scenario where I would use this tool.

The writing is clear, the software appears to be well designed, and it is open source. Below are some comments as suggestions for improving the paper.

- Figure 1 seems a bit superfluous to me. It attempts to provide a high-level justification for the tool, but in my opinion, it doesn't add anything to the paper beyond what is already in the text.

- The paper focuses mostly on justifying the need for the tool. But it provides little insight on *how* the tool works. For example, how does it collect the metadata and integrate everything? How does it integrate with snakemake? Etc. I don't think it's necessary to provide a lot more detail. But a little more would be helpful.

- The paper says, "Additionally, maintaining a simple project structure suitable for version control, further eases the adoption of Continuous Analysis on version control platforms (e.g., GitHub, GitLab, BitBucket, etc.)." I'm not sure if I understand exactly what this is saying. How does it support using version control?

- I'm probably missing it, but I don't see any explicit instructions about how to install the software. That's a pretty standard thing to see on documentation sites.

Reviewer #3: Computational analyses are getting a central part in an ever increasing number of scientific experiments and the amount and complexity of code that is produced is often difficult to maintain, distribute and replicate in a standard way.

In this manuscript the authors present a tools for easy integration, maintenance and organisation of multiple computational notebooks linked to complex analysis tasks. The tool functionalities are well structured and provide a way to add a layer of organisation to code without affecting the internal logic of existing components. The manuscript is clear and well written.

I think that, if adopted, the proposed tool can bring a considerable benefit to the research community.

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Reviewer #1: Yes: Hugo López-Fernández

Reviewer #2: No

Reviewer #3: No

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Scikick: a sidekick for workflow clarity and reproducibility during extensive data analysis

PONE-D-23-11089R1

Dear Dr. Oh,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Anna Bernasconi, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Dear authors,

your revised manuscript has been re-assessed by two reviewers and myself. We gladly recommend the paper for acceptance.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: All comments have been addressed so the paper can be accepted now. I do not have anything else to add.

Reviewer #2: I have no additional comments.This form is asking me to write a statement that is at least 100 characters long, but I have nothing else to say... :)

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Hugo López-Fernández

Reviewer #2: Yes: Stephen Piccolo

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