Free SKILL.md scraped from GitHub. Clone the repo or copy the file directly into your Claude Code skills directory.
npx versuz@latest install brycewang-stanford-awesome-agent-skills-for-empirical-research-skills-29-quarcs-lab-project20xxy-dot-claude-skills-submission-pgit clone https://github.com/brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research.gitcp Awesome-Agent-Skills-for-Empirical-Research/SKILL.MD ~/.claude/skills/brycewang-stanford-awesome-agent-skills-for-empirical-research-skills-29-quarcs-lab-project20xxy-dot-claude-skills-submission-p/SKILL.md---
name: submission-prep
description: 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
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`:
```bash
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:**
```markdown
## 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.