Full research pipeline from idea to paper. Orchestrates all phases — discovery, strategy, analysis, writing, peer review, and submission. Use when starting a new research project from scratch.
Scanned 9/3/2026
Install to Claude Code
npx -y skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill new-project --agent claude-codeInstalls into .claude/skills of the current project.
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---
name: new-project
description: Full research pipeline from idea to paper. Orchestrates all phases — discovery, strategy, analysis, writing, peer review, and submission. Use when starting a new research project from scratch.
argument-hint: "[research topic or 'interactive' for guided start]"
allowed-tools: Read,Grep,Glob,Write,Edit,Bash,Task,WebSearch,WebFetch
---
# New Project
Launch a full research pipeline from idea to paper, orchestrated through the dependency graph.
**Input:** `$ARGUMENTS` — a research topic or `interactive` for a guided start via `/discover interview`.
---
## Pipeline Overview
This skill orchestrates the full dependency graph. Each phase activates when its dependencies are met. The orchestrator manages agent dispatch, three-strikes escalation, and quality gates.
```
Phase 1: Discovery
├── /discover interview → Research Spec + Domain Profile
├── /discover lit → Literature Synthesis + BibTeX
└── /discover data → Data Assessment
Phase 2: Strategy (depends on Phase 1)
└── /strategize → Strategy Memo + Robustness Plan
Phase 3: Execution (depends on Phase 2)
├── /analyze → Scripts + Tables + Figures
└── /write → Paper Sections
Phase 4: Peer Review (depends on Phase 3)
├── /review --all → Comprehensive Quality Score
└── /review --peer → domain-referee + methods-referee Reports
Phase 5: Submission (depends on Phase 4, score >= 95)
├── /submit target → Journal Recommendations
├── /submit package → Replication Package
└── /submit final → Final Verification
```
---
## Workflow
### Step 0: Enter Plan Mode
Before any work begins:
1. **Enter plan mode** — use `EnterPlanMode`
2. **Create the project folder structure** — `data/raw/`, `data/cleaned/`, `scripts/R/`, `paper/sections/`, `paper/figures/`, `paper/tables/`, etc.
3. **Draft a high-level plan** — what phases are needed, estimated scope
4. **Save to disk** — `quality_reports/plans/YYYY-MM-DD_new-project.md`
5. **Present to user** — wait for approval before proceeding
6. **Exit plan mode** — only after approval
### Step 1: Discovery Phase
1. **If `interactive` or no research spec exists:**
Run `/discover interview` to produce:
- Research specification (`quality_reports/research_spec_*.md`)
- Domain profile (`.claude/references/domain-profile.md`) — if still template
2. **Run `/discover lit`** with the research topic:
- Librarian collects literature
- librarian-critic reviews coverage
- Output: literature synthesis + BibTeX entries
3. **Run `/discover data`** to find datasets:
- Explorer searches for data sources
- explorer-critic assesses data quality
**Gate:** Research spec and literature review must exist before proceeding.
### Step 2: Strategy Phase
4. **Run `/strategize`** to design the empirical strategy:
- Strategist proposes identification strategy
- strategist-critic validates the design
**Gate:** Strategy memo must pass strategist-critic review (score >= 80).
### Step 3: Execution Phase
5. **Run `/analyze`** to implement the strategy:
- Data-engineer cleans data and creates figures
- Coder writes analysis scripts
- coder-critic reviews code
6. **Run `/write`** to draft the paper:
- Writer drafts sections
- Humanizer pass strips AI patterns
**Gate:** Code must pass coder-critic review. Paper sections must exist.
### Step 4: Peer Review Phase
7. **Run `/review --all`** for comprehensive review:
- strategist-critic + coder-critic + writer-critic + Verifier in parallel
- Weighted aggregate score computed
8. **Run `/review --peer`** for simulated peer review:
- domain-referee (subject expertise) + methods-referee (econometrics)
- Independent, blind reports
- Orchestrator synthesizes editorial decision
**Gate:** Aggregate score >= 80 (commit-ready). Score >= 90 for submission.
### Step 5: Submission Phase (optional, user-triggered)
9. **Run `/submit target`** for journal recommendations
10. **Run `/submit package`** for replication package
11. **Run `/submit final`** for final verification
---
## User Interaction Points
The pipeline pauses for user input at these points:
- After interview (approve research spec)
- After strategy memo (approve identification strategy)
- After data analysis (review results before paper drafting)
- After peer review (review feedback before revision)
- Before submission (approve journal choice)
Between pauses, the orchestrator runs autonomously per `workflow.md`.
---
## Principles
- **This is always orchestrated.** Unlike other skills, `/new-project` always runs through the full pipeline.
- **Dependency-driven.** Phases activate by dependency, not forced sequence.
- **Quality-gated.** Each phase transition requires passing quality checks.
- **User retains control.** Pipeline pauses at key decision points.
- **Resumable.** If interrupted, the pipeline resumes from the last completed phase.
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