JOSS submission checklist

This repository includes a short JOSS-style paper draft in paper/.

Current status: technically prepared, but do not submit to JOSS yet. The paper, metadata, release archive, and paper-build workflow are in place. The missing piece is time: current JOSS pre-review screening requires more than six months of public development history, with active work spread across that period. This repository’s first commit is dated 2026-05-25, so the earliest reasonable submission window is after 2026-11-25, assuming development and public release activity continues.

This should be treated as a real gate, not a paperwork detail. Submitting before there is enough public history would likely waste reviewer/editor time and risk a desk rejection for a reason we can already see.

Before submitting later:

  • Confirm the current public release is archived and citable. Current release DOI: https://doi.org/10.5281/zenodo.20541928.

  • Confirm the repository still satisfies the current JOSS pre-review gates: public development history, demonstrated research use, active open-source practices, tests, documentation, releases, contribution/support expectations, and sustained iteration over time.

  • Confirm there is visible public activity after 2026-05-25: tagged releases, issues or PRs where useful, changelog entries, CI history, documentation improvements, and evidence that the software has been refined through use.

  • Confirm the paper still makes honest claims. Do not add adoption, clinical, scientific-discovery, or general Picard-replacement claims unless there is public evidence to support them.

  • Confirm the paper metadata still matches the repository metadata: author name, independent researcher affiliation, software version, and DOI.

  • Run the local paper check:

    python3 tools/verify_joss_paper.py

  • Confirm the JOSS Paper GitHub Actions workflow builds paper/paper.pdf.

  • Confirm the main CI workflow is green.

  • Confirm the Bioconda PR or package status is accurately described in Packaging before submission.

  • Submit through the JOSS form with:

    • repository: https://github.com/dnncha/turbo-picard

    • paper path: paper/paper.md

    • archive DOI: 10.5281/zenodo.20541928

    • conflict of interest: none, unless that changes before submission

    • related publications: none, unless a Bioinformatics/BMC/preprint submission exists by then

After acceptance, update the README, documentation, CITATION.cff, and Zenodo metadata with the JOSS paper DOI. Until then, cite the Zenodo software DOI.

Useful JOSS links: