[PRE REVIEW]: Tataki: Enhancing the robustness of bioinformatics workflows with simple, tolerant file format detection

[editorialbot]

Submitting author: @fmaccha (Masaki Fukui)
Repository: https://github.com/sapporo-wes/tataki
Branch with paper.md (empty if default branch): joss_paper
Version: v0.5.1
Editor: Pending
Reviewers: Pending
Managing EiC: Arfon Smith

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1829f4731e0258b8edb5983899db7455/status.svg)](https://joss.theoj.org/papers/1829f4731e0258b8edb5983899db7455)

Author instructions

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

@fmaccha 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.

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[editorialbot]

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

✅ OK DOIs

- 10.1145/3486897 is OK
- 10.1109/ICSE55347.2025.00158 is OK
- 10.1093/bioinformatics/btac327 is OK
- 10.1038/d41586-019-02619-z is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/nar/gks1175 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.1016/j.xgen.2021.100029 is OK
- 10.1093/bioinformatics/btq351 is OK
- 10.7490/f1000research.1118900.1 is OK
- 10.1371/journal.pcbi.1009823 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Fine Free File Command (and libmagic) — darwinsys....

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Repository Analysis Report

Code breakdown

github.com/AlDanial/cloc v 1.98  T=0.03 s (1733.8 files/s, 169230.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                            25            389            272           2029
CSV                              5              0              0            740
Markdown                         7            207              0            543
YAML                             5             18              6            220
TeX                              1             12              0            156
TOML                             1              3              1             44
Dockerfile                       1              8              1             20
Python                           1              2              0              6
Bourne Shell                     1              3              1              3
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            48            642            281           3762
-------------------------------------------------------------------------------

Commit Count by Author

83	fmaccha
     6	suecharo
     3	Igor Martayan
     2	m4tty4
     1	Hirotaka Suetake
     1	Tazro Inutano Ohta

Repository History

Repository age: First commit on September 04, 2022

GitHub Activity Metrics

Metric	Count
GitHub stars	6
Forks	2
GitHub contributors	3
Releases	12
Total issues	7
Total pull requests	8
Unique commenters/reviewers (excluding authors)	2

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1256

✅ The paper includes a Statement of need section

🔴 Failed to discover a `Software Design` section in paper

🔴 Failed to discover a `Research Impact Statement` section in paper

🔴 Failed to discover an `AI usage disclosure` section in paper

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

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[arfon]

Update regarding JOSS scope and paper format changes

👋 @fmaccha. Thank you for your patience while your submission has been waiting in our pre-review queue.
We're writing to let you know that JOSS has updated its submission requirements and scope criteria. You can read the full details in our blog post: https://blog.joss.theoj.org/2026/01/preparing-joss-for-a-generative-ai-future

What this means for your submission

As your submission is currently in pre-review, it will be evaluated against the updated scope. Before we can proceed, we need you to update your paper to match our new required format.

JOSS papers now require the following additional sections:

• Software Design (~200 words): Explain the trade-offs you weighed, the design/architecture you settled on, and why it matters. If other packages exist in this space, you must include an explicit "build vs. contribute" justification explaining why you created new software rather than contributing to existing projects.
• Research Impact Statement (~200 words): Provide concise evidence of either realized impact (e.g., external use, integrations, enabled results) or credible near-term significance (novel capability with benchmarks, reproducible materials, and community-readiness signals such as documentation, tests, license, releases, and contribution process).
• AI Usage Disclosure: Disclose any use of generative AI in your submission, including software creation, documentation generation, or paper authoring. If you did not use AI tools, please state this explicitly.

For full details, please see:

• Our updated scope definition: https://joss.readthedocs.io/en/latest/submitting.html#scope-and-significance
• An example paper in the new format: https://joss.readthedocs.io/en/latest/example_paper.html

Important: Once you have updated your paper, please comment here to let us know. At that point, we will assess your software against our updated scope criteria. We want to be transparent that under these new criteria, some submissions that were previously in scope may now be deemed out of scope, and we may choose not to proceed with review.

We understand this may be frustrating, particularly if you've been waiting for some time. We apologise for that. These changes reflect the rapidly evolving landscape of software development and our commitment to ensuring JOSS publications recognise genuine scholarly contributions.

If you have any questions, please don't hesitate to ask.

[arfon]

Apologies, we missed one section from the list above. In addition to the sections already mentioned, JOSS papers now also require:

• State of the Field (~200 words): A description of how this software compares to other commonly-used packages in the research area. If related tools exist, provide a clear "build vs. contribute" justification explaining your unique scholarly contribution and why existing alternatives are insufficient.

So in summary, the requested additions are:

1. State of the Field (~200 words): A description of how this software compares to other commonly-used packages in the research area. If related tools exist, provide a clear "build vs. contribute" justification explaining your unique scholarly contribution and why existing alternatives are insufficient.
2. Software Design (~200 words): An explanation of the trade-offs you weighed, the design/architecture you chose, and why it matters for your research application. This should demonstrate meaningful design thinking beyond a superficial code structure description.
3. Research Impact Statement (~200 words): Evidence of realized impact (publications, external use, integrations) or credible near-term significance (benchmarks, reproducible materials, community-readiness signals). The evidence should be compelling and specific, not aspirational.
4. AI Usage Disclosure: Transparent disclosure of any use of generative AI in the software creation, documentation, or paper authoring. If no AI tools were used, state this explicitly. If AI tools were used, describe how they were used and how the quality and correctness of AI-generated content was verified.

Apologies again for the oversight.

[fmaccha]

Hello! Thanks for the update. I have been working on the paper based on the previous requirements and will update it to match the new format. I will notify you once the update is complete.

[rkurchin]

Hi @fmaccha, AEiC for the BCM track here just dropping in to let you know that we've got a bit of a backlog on our track at the moment and so I'll have to waitlist this submission for now until an appropriate editor becomes available.

[fmaccha]

@editorialbot generate pdf