claude-code-my-workflow is a forkable setup for using Claude Code to produce and review academic papers, slides, data analyses, and replication packages. Researchers use its agents, skills, rules, hooks, and quality checks to coordinate these tasks and verify their results. The catalogue entries define the reusable workflow components for Claude Code.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add pedrohcgs/claude-code-my-workflow --skill audit-reproducibilitygit clone --depth 1 https://github.com/pedrohcgs/claude-code-my-workflowWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pedrohcgs/claude-code-my-workflow/audit-reproducibility)<a href="https://agentmods.dev/skills/pedrohcgs/claude-code-my-workflow/audit-reproducibility"><img src="https://agentmods.dev/badge/skills/pedrohcgs/claude-code-my-workflow/audit-reproducibility/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pedrohcgs/claude-code-my-workflow/audit-reproducibility"><img src="https://agentmods.dev/badge/skills/pedrohcgs/claude-code-my-workflow/audit-reproducibility.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 6 findings, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Agent Snooping · line 286 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 287 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 288 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 289 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 290 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 290 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00054 | $0.05865 |
| Opus 5 | $0.00027 | $0.02933 |
| Sonnet 5 | $0.00011 | $0.01173 |
| Haiku 4.5 | $0.00005 | $0.00587 |
Grade A, and why
audit-reproducibility scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 301 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Audit Reproducibility
Compare numeric claims in a manuscript (point estimates, standard errors, p-values, counts) against the actual outputs produced by the analysis pipeline. Report PASS / FAIL per claim against the tolerance thresholds defined in .claude/rules/replication-protocol.md.
Core principle: If the paper says ATT = -1.632 (0.584) and the code produces -1.628 (0.591), we verify — numerically — that the difference is within the documented tolerance. No more "looks close enough" eyeballing.
Two directions, not one. Vertically, each claim is checked against the output that produced it. Horizontally, it is checked against every other artifact that displays the same number — the supplement table, the slide deck, the poster. The vertical check passes contentedly while a deck quotes last month's value; only the horizontal one catches that. Declared displays live in the passport's appears_in list — see replication-protocol.md → The horizontal check.
When to use
- Before submission. Catches the "I updated the analysis but forgot to update Table 2" bug.
- Before presenting or teaching from the same numbers. Catches the deck, the poster, or the supplement that was never regenerated after the last rerun.
- Before releasing a replication package. Verifies the code actually reproduces the paper.
- After a major revision. Ensures the paper still matches the latest code.
- Quality-gate in
/commit. Pair with a pre-commit invocation on manuscript + analysis changes.
Inputs
$0— path to the manuscript (.tex,.qmd,.md,.pdf). Required.$1— path to the outputs directory. Defaults toscripts/R/_outputs/. Recognised alternatives:scripts/stata/_outputs/(Stata pipelines built by/stata-replication),_targets/objects/(Rtargetsworkflows), any directory the user-specified outputs live in.
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 301 lines · 54 tokens per session scan A 5c6c489bde5c
audit-reproducibility is a skill published in the GitHub repository pedrohcgs/claude-code-my-workflow (1,569 stars, last pushed 15d ago), licensed MIT. It adds 54 tokens to every session and 5,865 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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