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 agentmods add skills/docxology/template/researchnpx skills add docxology/template --skill researchgit clone --depth 1 https://github.com/docxology/templateWrote 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/docxology/template/research)<a href="https://agentmods.dev/skills/docxology/template/research"><img src="https://agentmods.dev/badge/skills/docxology/template/research.svg" alt="Measured on agentmods" height="20"></a>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 | $0.00091 | $0.01008 |
| Opus 5 | $0.00046 | $0.00504 |
| Sonnet 5 | $0.00018 | $0.00202 |
| Haiku 4.5 | $0.00009 | $0.00101 |
Grade A, and why
research-workflow 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 2d 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 — 132 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Research Workflow
Seven-stage research workflow scaffolding for AI-assisted research processes. Each stage produces structured prompts and acceptance criteria for agent loops.
Stages
| # | Stage | Purpose |
|---|---|---|
| 1 | SCOPE | Define research question, scope, and success criteria |
| 2 | LITERATURE | Survey prior work; produce annotated bibliography |
| 3 | REASON | Identify gaps, contradictions, and open questions |
| 4 | DESIGN | Formulate methodology and experimental plan |
| 5 | COMPUTE | Execute analysis; collect and validate results |
| 6 | SYNTHESIZE | Interpret results relative to prior work |
| 7 | WRITE | Draft manuscript sections and iterative revision |
Quick Start
from infrastructure.research import ResearchWorkflow
# Print all stage descriptions
ResearchWorkflow.describe()
# Get a structured prompt for a specific stage
prompt = ResearchWorkflow.prompt("SCOPE", question="What drives protein misfolding?")
print(prompt)
# Iterate stages in order
for stage in ResearchWorkflow.stages():
print(f"{stage.index}. {stage.name}: {stage.description}")
Pipeline Orchestrator
# Run research workflow scaffolding for a named project
uv run python scripts/pipeline/stage_10_research_workflow.py --project my_project
# Run only specific stages
uv run python scripts/pipeline/stage_10_research_workflow.py --project my_project --stages SCOPE,LITERATURE
# Generate stage prompts without executing
uv run python scripts/pipeline/stage_10_research_workflow.py --project my_project --dry-run
Config Integration
Set stage overrides in projects/{name}/manuscript/config.yaml:
research_workflow:
question: "How do transformer attention patterns relate to syntactic structure?"
stages:
SCOPE:
depth: detailed
LITERATURE:
max_papers: 50
sources:
- arxiv
- semantic_scholar
WRITE:
target_venue: NeurIPS
Key Types
from infrastructure.research import (
ResearchWorkflow, # instance API — workflow.stage(name) / all_stages() / describe()
ResearchStage, # Stage descriptor: name, label, description, inputs, outputs, gate, status, order
ResearchWorkflowConfig, # Parsed config.yaml `research_workflow:` block
)
What ships with it
9 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.
- 2d ago First seen · 132 lines · 91 tokens per session scan A 933aa1c43d22
research-workflow is a skill published in the GitHub repository docxology/template (19 stars, last pushed today), licensed Apache-2.0. It adds 91 tokens to every session and 1,008 once invoked, about $0.0005 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 2026-09-03.
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