← LeaderboardThe Skill Leaderboard

submission-prep

Runs pre-submission checks (word count, anonymization, citations, placeholders, cross-refs) and generates a checklist. Use before journal submission.

Published by brycewang-stanford ↗brycewang-stanford/Auto-Empirical-Research-Skills

Try your first task

submission-prep

Start a fresh conversation.

Use submission-prep to run the pre-submission checks for the manuscript and produce a submission checklist with pass/fail results for automated checks and unchecked manual items.

    User-approved starter prompt based on a pinned source version; check current skill requirements before running. Task evidence ↗

    SKILL.md

    name: submission-prepdescription: Runs pre-submission checks (word count, anonymization, citations, placeholders, cross-refs) and generates a checklist. Use before journal submission.allowed-tools: Bash, Read, Write, Edit, Glob, Grep

    Prepare for Submission

    Run pre-submission checks and generate a submission checklist for a journal submission.

    Steps

    1. Render the manuscript if _manuscript/ does not exist or is stale:

      bash scripts/render.sh

    2. Word count — Count words in the prose body of index.qmd:

      • Exclude YAML front matter, code blocks, embed shortcodes, and the References section
      • Report: total word count, and breakdown by section
      • Flag if over common limits (8,000 or 10,000 words)

    3. Anonymization check — Scan index.qmd for content that may violate double-blind review:

      • Author names (from the YAML author field) appearing in the body text
      • First-person self-citations (e.g., "our previous work", "we showed in Author (Year)")
      • Acknowledgments section content that identifies the authors
      • Repository URLs that reveal author identity
      • Report each finding with line numbers

    4. Citation audit — Cross-check citations and references:

      • Extract all @key and [@key] citations from index.qmd
      • Extract all keys from references.bib
      • Report:
        • Citations used in text but missing from .bib (errors)
        • Entries in .bib not cited in the manuscript (unused — informational only)

    5. Figures and tables inventory — List all embedded outputs:

      • Extract all {{< embed >}} shortcodes from index.qmd
      • For each, check that the referenced notebook and cell label exist
      • Report a table: label, notebook, caption (from cell directive), type (figure/table)

    6. Placeholder check — Scan for orphan [FILL:] placeholders in index.qmd:

      grep -n "\[FILL:" index.qmd

      Report each with line number and context.

    7. Cross-reference check — Scan for @sec-, @fig-, @tbl- references in index.qmd and verify each target exists (section IDs in the document, figure/table labels in notebooks).

    8. Generate submission checklist:

      ## Submission Checklist

- [ ] Word count within journal limit: <count> words
- [ ] No anonymization issues (or list issues to fix)
- [ ] All citations resolve to references.bib entries
- [ ] No orphan [FILL:] placeholders in manuscript
- [ ] All embedded figures/tables have valid notebook sources
- [ ] All cross-references resolve
- [ ] Abstract present and complete
- [ ] Keywords listed
- [ ] Acknowledgments section reviewed
- [ ] Data availability statement included
- [ ] PDF renders without errors
- [ ] Figures are high resolution
- [ ] Supplementary materials prepared (if applicable)

    9. Report the full checklist with pass/fail status for each automated check, and leave manual items unchecked for the user.