Deep Research Pipeline

Multi-stage deep research with reflection loops, multi-query retrieval, LLM chunk selection, and citation integrity. Use when: deep research, literature review, topic investigation, multi-source analysis, fact-checking, competitive analysis, technology deep-dives.

Deep Research Pipeline turns broad questions into cited, publication-quality reports through a staged research workflow: planning, multi-query retrieval, chunk selection, analysis, reflection, writing, and optional verification.

It is designed for research that should not be answered from memory or a single search result. The pipeline keeps claims tied to sources, surfaces contradictions, tracks gaps, and can resume from checkpoints.

Why Use It

• Multi-stage research, not one-shot summarization — separate researcher, analyst, reflection, and writer stages.
• Citation integrity — findings and final claims trace back to URLs/sources.
• Reflection loops — the pipeline checks coverage and decides whether another cycle is needed.
• Portable LLM config — supports LLM_API_KEY/LLM_API_BASE, OpenAI-compatible endpoints, or Z.AI GLM.
• Operational controls — checkpoint/resume, time limits, token budgets, output formats, and mock mode.

When to Use

Deep research, comprehensive analysis, literature reviews, competitive analysis, fact-checking, technology deep-dives — anything needing multiple sources, synthesis, and verified citations.

Quick Start

bash

cd skills/deep-research

# Optional: configure any OpenAI-compatible provider
export LLM_API_KEY="your-key"
export LLM_API_BASE="https://api.example.com/v1"
export LLM_MODEL="your-model"

# Or use OpenAI-compatible env names
export OPENAI_API_KEY="your-key"
export OPENAI_BASE_URL="https://api.example.com/v1"

# Run a report
python3 scripts/research_pipeline.py \
  "Compare Vercel, Netlify, and Cloudflare Pages in 2026" \
  --max-cycles 2 \
  --format report \
  --output report.md

# Test without API calls
python3 scripts/research_pipeline.py "test question" --mock --output report.md

If no universal/OpenAI-compatible variables are set, the skill still supports Z.AI via ZAI_API_KEY and ZAI_API_ENDPOINT.

Architecture

text

ORCHESTRATOR (you)
    │
    ├── Plan → Decompose question into research dimensions
    │
    ├── REFLECTION LOOP (0-8 cycles)
    │   ├── Researcher Agent (parallel) → multi-query search + chunk selection
    │   ├── Analyst Agent → dedupe + themes + contradictions
    │   └── Reflection → coverage check, gap analysis, continue decision
    │
    ├── Writer Agent → polished report (report/summary/brief/json)
    │
    └── Verify (optional) → adversarial fact-check

Key principle: Orchestrator NEVER searches directly. Clean output flows between stages only.

Two Modes

Mode 1: Full Pipeline CLI (Recommended)

Use the enhanced research_pipeline.py for automated end-to-end research:

bash

# Full research with all features
python3 scripts/research_pipeline.py "What is the state of quantum computing in 2026?" \
    --max-cycles 3 \
    --output report.md \
    --format report

# Mock mode (no API calls, for testing)
python3 scripts/research_pipeline.py "test question" --mock --output report.md

# With budget limits
python3 scripts/research_pipeline.py "question" \
    --max-cycles 3 --time-limit 300 --token-limit 40000

# Resume from checkpoint
python3 scripts/research_pipeline.py "question" \
    --resume checkpoint.json --output report.md

# Explicit dimensions
python3 scripts/research_pipeline.py "question" \
    --dimensions architecture benchmarks limitations \
    --output report.md --format summary

CLI Flags:

Flag	Default	Description
--max-cycles	3	Max research cycles (1-8)
--mock	false	Use mock data, no API calls
--output / -o	stdout	Output file path
--format / -f	report	Output format: report, summary, brief, json
--time-limit	900	Max seconds for entire pipeline
--token-limit	60000	Max estimated tokens
--checkpoint	none	Save checkpoints to path
--resume	none	Resume from checkpoint file
--dimensions	auto	Explicit research dimensions
--no-parallel	false	Research dimensions sequentially

Output formats:

• report — Full markdown: Executive Summary → Key Findings → Detailed Analysis → Contradictions → Gaps → Sources → Methodology
• summary — Executive summary + top 5 findings + sources
• brief — Bullet-point format for quick scanning
• json — Structured JSON with annotated findings and metadata

Mode 2: Orchestrated Sub-Agents (For complex research)

Use when you need fine-grained control over each stage or parallel dimension research with sub-agents.

Workflow (Orchestrated Mode)

Phase 1: Planning

• Analyze question, create slug, make memory/research/<slug>/ directory
• Generate research plan with dimensions and questions
• Save to plan.md

Phase 2: Research Cycle (repeat up to 8 times)

Step A: Spawn Researcher Agent(s)

Use sessions_spawn with a task brief (NOT the full query):

json

{
  "dimension": "technical architecture",
  "specific_questions": ["How does X work?", "What are Y's components?"],
  "context_limit": 5000,
  "max_sources": 10
}

Researcher agent does:

1. Multi-query generation — scripts/query_generator.py produces 3-5 variants
2. Parallel search — web_search for each variant
3. Content fetching — web_fetch for top results
4. LLM chunk selection — scripts/chunk_selector.py scores each chunk (≥0.7)
5. Context expansion — scripts/context_expander.py fetches surrounding content
6. Output: JSON findings with citations

Can spawn 2-3 researcher agents in parallel for different dimensions.

Step B: Spawn Analyst Agent

After researcher(s) complete, spawn analyst with their combined output:

1. Deduplicate overlapping findings
2. Flag contradictions (explicit + implicit)
3. Group into thematic clusters
4. Identify gaps
5. Output: Cleaned JSON + gap list

Step C: Run Reflection

After analyst completes, run scripts/reflection.py:

1. What's covered? (themes + confidence scores)
2. What gaps remain? (unanswered questions)
3. What contradictions emerged?
4. New directions discovered?
5. Should continue? (coverage ≥ 0.8 + minor gaps → stop)

Save reflection to memory/research/<slug>/reflection-cycle-N.md

Continue Decision

• Coverage ≥ 0.8 AND gaps minor → proceed to Phase 3
• Major contradictions → spawn targeted researcher
• Significant gaps → another researcher cycle
• Hard stop at cycle 8

Phase 3: Write Report

Use the Writer Agent (scripts/writer.py) for publication-quality output:

python

# From Python
from writer import WriterAgent, OutputFormat, write_report

# Generate report using WriterAgent
agent = WriterAgent(use_llm=True)
result = agent.write_report(
    analyst_output,           # from analyst or run_analyst()
    question="What is RAG?",
    fmt=OutputFormat.REPORT,
)

# Or use convenience function
result = write_report(analyst_output, question, fmt="report")

# Save to file
from writer import save_report
save_report(result, "output/report.md")

Report features:

• 🟢🟡🟠🔴 Confidence indicators on every finding
• [source_url] inline citations throughout
• ⚠️ Contradiction callout boxes where sources disagree
• Structured sections: Summary → Findings → Analysis → Contradictions → Gaps → Sources → Methodology
• Template-based fallback when no LLM available

Phase 4: Verify (optional sub-agent)

Spawn adversarial verifier:

• Anchor every claim to source
• Verify URLs with web_fetch
• Remove unsourced claims
• Save to review.md

Phase 5: Deliver

• Fix any FATAL issues from review
• Copy to final.md
• Write provenance.md (date, cycles, sources, verification status)
• Send summary to user

Python API

python

import sys, os
sys.path.insert(0, os.path.expanduser("~/.openclaw/workspace/skills/deep-research/scripts"))

from research_pipeline import run_enhanced_pipeline

result = run_enhanced_pipeline(
    question="What is the state of quantum computing in 2026?",
    max_cycles=3,
    dimensions=["hardware", "algorithms", "applications", "challenges"],
    mock_mode=False,
    output_format="report",
    time_limit=900,
    token_limit=60000,
    checkpoint_path="checkpoint.json",    # auto-saves progress
    parallel_dimensions=True,             # parallel research per dimension
)

# result["report"] = markdown string
# result["cycles_completed"] = int
# result["final_coverage"] = float (0.0-1.0)
# result["metadata"] = dict with timing, findings count, etc.

Scripts

Script	Purpose	Usage
research_pipeline.py	Full pipeline orchestration	python3 scripts/research_pipeline.py "question" --max-cycles 3
query_generator.py	Generate 3-5 search query variants	python3 scripts/query_generator.py -q "..."
chunk_selector.py	LLM scores chunks, filters by threshold	python3 scripts/chunk_selector.py -q "..." -c chunks.json
context_expander.py	Fetch surrounding context for incomplete chunks	python3 scripts/context_expander.py -s selected.json -q "..."
reflection.py	Mandatory gap/contradiction check	python3 scripts/reflection.py -q "..." -f findings.json -c 1
writer.py	Publication-quality report generation	from writer import WriterAgent, write_report
analyst.py	Dedup + themes + contradictions (no API needed)	from analyst import analyze_findings
researcher.py	Multi-source research orchestration	from researcher import research, research_dimension
research_sources.py	Search adapters (web, GitHub, docs)	from research_sources import WebSearchSource
fact-checker.py	Claim extraction + source ranking	python3 scripts/fact-checker.py "text" --sources '["url1"]'

All LLM-enabled scripts use the shared provider-agnostic llm_client.py.

Provider resolution order:

1. LLM_API_KEY + LLM_API_BASE + optional LLM_MODEL
2. OPENAI_API_KEY + OPENAI_API_BASE / OPENAI_BASE_URL + optional OPENAI_MODEL
3. ZAI_API_KEY + optional ZAI_API_ENDPOINT / GLM_MODEL

If no key is configured, use --mock for local pipeline testing or rely on scripts with rule-based fallbacks where available.

Examples

Example 1: Quick Competitive Analysis

bash

python3 scripts/research_pipeline.py \
    "Compare Vercel vs Netlify vs Cloudflare Pages features and pricing 2026" \
    --max-cycles 2 \
    --dimensions features pricing performance ecosystem \
    --format summary \
    --output competitive-analysis.md

Example 2: Deep Technology Research

bash

python3 scripts/research_pipeline.py \
    "What is the current state of AI agent frameworks?" \
    --max-cycles 4 \
    --time-limit 600 \
    --token-limit 80000 \
    --checkpoint /tmp/ai-agents-checkpoint.json \
    --format report \
    --output ai-agents-research.md

Example 3: Literature Review (mock mode for testing)

bash

python3 scripts/research_pipeline.py \
    "What does the research say about transformer architecture efficiency?" \
    --mock \
    --max-cycles 3 \
    --format report \
    --output literature-review.md

Example 4: Bullet Brief for Quick Scanning

bash

python3 scripts/research_pipeline.py \
    "What are the latest developments in Rust web frameworks?" \
    --max-cycles 2 \
    --format brief \
    --output rust-web-brief.md

Example 5: JSON Output for Programmatic Use

bash

python3 scripts/research_pipeline.py \
    "What is the market size of edge computing?" \
    --max-cycles 2 \
    --format json \
    --output edge-computing-data.json

Integration with Night Shift

To queue research plans for Night Shift execution:

1. Create a research plan file:

json

// memory/research/queued/<slug>.json
{
  "question": "What is the state of quantum computing in 2026?",
  "max_cycles": 3,
  "dimensions": ["hardware", "algorithms", "applications"],
  "output_format": "report",
  "output_path": "memory/research/quantum-2026/final.md",
  "time_limit": 600,
  "created_at": "2026-04-25T06:00:00Z"
}

2. Night Shift picks up queued plans and runs them via:

bash

python3 scripts/research_pipeline.py "$QUESTION" \
    --max-cycles $MAX_CYCLES \
    --dimensions $DIMENSIONS \
    --format $FORMAT \
    --output $OUTPUT_PATH \
    --time-limit $TIME_LIMIT

3. Results are saved to memory/research/<slug>/final.md with provenance metadata.

File Layout

text

memory/research/<slug>/
├── plan.md                    # Research plan with dimensions
├── reflection-cycle-1.md      # Reflection after each cycle
├── reflection-cycle-2.md
├── researcher-output-*.json   # Raw researcher findings
├── analyst-output.json        # Merged/deduped findings
├── draft.md                   # First draft
├── brief.md                   # Verified brief
├── review.md                  # Adversarial review (optional)
├── final.md                   # Final report
├── provenance.md              # Metadata + source verification status
└── checkpoint.json            # Pipeline checkpoint (auto-saved)

Quick Mode

Skip sub-agents and the full pipeline. Do 5-10 searches yourself. Still use evidence tables, verify URLs, cite sources. Shorter, inline in chat.

Integrity Commandments

1. Never fabricate a source — no URL = don't mention it
2. Never claim existence without checking
3. Never extrapolate unread details
4. Read before summarizing
5. No fake certainty — never say "verified" unless checked
6. Never invent numbers/benchmarks/comparisons
7. Separate observations from inferences
8. Every claim traces to a source — citation integrity is mandatory
9. Reflection is not optional — run it after every cycle
10. Stage separation — orchestrator never searches, researchers never see full plan

Scale Decision

• Single fact → Quick Mode (3-10 tool calls, no sub-agents)
• 2-3 item comparison → 2 parallel researcher sub-agents, 2-3 cycles
• Broad/multi-faceted → 3-4 researcher sub-agents, 3-5 cycles
• PhD-level deep dive → 4+ researchers, 5-8 cycles

See Also

• DOCS.md — Full API reference, architecture diagrams, troubleshooting
• test_integration.py — 29 integration tests covering the full pipeline
• test_pipeline.py — 26 unit tests for individual components