| name | research-pipeline |
| description | End-to-end reproducible academic-paper research using the research-pipeline CLI and MCP server. Plans queries, searches arXiv/Google Scholar/Semantic Scholar/OpenAlex/DBLP/HuggingFace, screens with BM25, downloads and converts PDFs to Markdown, extracts evidence, summarizes, validates, and writes a human-readable, evidence-cited research report. Iterates up to 4 rounds to close academic and engineering gaps, and resumes on top of any prior same-topic report. Use when the user asks to "research", "find papers", "survey the literature", "do a literature review", "analyze arXiv papers", "build a research report", "screen papers", "summarize papers", "expand citations", "fill research gaps", or "resume a prior research report". Do NOT use for general web search, simple PDF-to-Markdown conversion (use `research-pipeline convert-file` directly), or requirements analysis (use the req-analysis skill).
|
| license | MIT |
Academic Paper Research
When To Trigger
- "Research
<topic>" / "Do a literature review on <topic>"
- "Find recent papers on
<topic>" / "Survey arXiv for <topic>"
- "Build a research report on
<topic>" / "Screen / summarize / synthesize papers"
- "Expand the citation graph" / "Resume the prior research report"
- "Close the gaps in the research report"
Do not trigger for general web search, single PDF conversion
(research-pipeline convert-file), requirements/architecture design
(use req-analysis), or single-paper explanation (use paper-analyzer).
Launch
Always launch through the manifest-governed runner. Never bypass it.
SKILL_DIR=~/.claude/skills/research-pipeline
CFG=$SKILL_DIR/config.toml
python3 $SKILL_DIR/runners/runner.py "<topic>" --config "$CFG"
The runner reads manifest.json, initialises workflow_state.json,
and drives all tasks in dependency order. Each task status is written
to workflow_state.json before the next task begins. Completion is
proved by artifact existence + schema validation — not by agent claim.
Rules
- Do not bypass the runner. Never call pipeline CLI commands
directly without the orchestrator updating
workflow_state.json.
- Resume = re-run the runner. Pass
--state <existing>.json to
continue an interrupted workflow. Idempotent: accepted tasks are skipped.
- Sub-agent delegation. When the runner prints
DELEGATE TO SUB-AGENT,
execute the named sub-agent with the printed contract, then update
workflow_state.json tasks.<id>.status = "accepted" and re-run.
- Reviewer gates. If a reviewer sub-agent returns
status: "rejected",
fix the artifact, reset the task to pending, and re-run. Do not
override a rejected verdict.
- Final report. Write
./<topic-slug>-research-report.md only after
validate-report is accepted. Never write it before that gate.
- Evidence-based. Every finding in the report must cite at least one
paper ID traceable to
screened.jsonl or analysis/.
References
| File | Load when |
|---|
references/workflow-steps.md | Per-agent SKILL_DIR paths, or understanding/diagnosing an orchestrated task |
references/command-reference.md | CLI options, profiles, MCP tool map, advanced flags |
references/query-optimization.md | Editing query_plan.json or weak recall |
references/sub-agents.md | Launching screener, analyzer, synthesizer |
references/output-templates.md | Writing or validating the final report |
references/iterative-synthesis.md | Gap-closure rounds and stopping conditions |
references/troubleshooting.md | Install/config/source/converter/MCP failures |
Final Response To User
When workflow_state.json shows status: complete:
- Show the final report path and the round-history table.
- List any remaining open gaps (ACADEMIC / ENGINEERING) not closed this run.
- Offer to run another round, expand citations, or hand off to
req-analysis.
