Agent skill

Deep Research Workflow

by TokenRhythm in TokenRhythm/opensquilla

Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations.

Apache-2.0Auto-check passedResearch & Science

Install Deep Research Workflow

skills CLI
$ npx skills add TokenRhythm/opensquilla --skill deep-research -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install TokenRhythm/opensquilla deep-research --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/TokenRhythm/opensquilla.git skills-src && mkdir -p .claude/skills && cp -r skills-src/src/opensquilla/skills/bundled/deep-research .claude/skills/deep-research && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
deep-research
GitHub stars
7.1k
Token cost
~1.3k tokens
SKILL.md length
467 words
Files
7 (incl. scripts, references)
Skills in repo
8
Repo updated
First seen
Licence
Apache-2.0

At a glance

Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations.

  • Works in 3 steps: Plan → Iterate → Compile
  • Producing a research report with a citation for each claim
  • SKILL.md covers Decide if this is the right tool, Stages, Stage 1: Plan and Stage 2: Iterate, plus 3 more sections
  • Runs Python scripts from its folder; calls python

What it does

The skill structures an investigation as plan, iterate and compile, with all progress kept in one JSON state file that can resume the work at any point. It does not fetch the web itself: it prints a fetch list for the host agent to run with its own web tools and records the evidence that comes back. It is meant for deep dives, research reports and literature reviews, where a single-pass summary would lose too much.

Planning splits a question into sub-questions according to a depth setting: overview, thorough or exhaustive, with 3-5, 6-10 or 12-20 sub-questions and growing source targets. Each iteration round records evidence and updates coverage per sub-question until the plan's done flag flips. Sources are judged on authority, recency, evidence, bias and corroboration. Compile then writes a Markdown report that starts with an executive summary. The plan.py, iterate.py and compile.py scripts do the work, with references on methodology and sources.

When your agent uses it

  • Producing a research report with a citation for each claim
  • Running a multi-round literature review that can be resumed
  • Scoping a broad question into sub-questions and tracking coverage

Example prompts

  • “Do a thorough deep dive on how vector databases handle filtered search and write a cited report.”
  • “Plan an exhaustive literature review on remote work and productivity, then start round one.”
  • “Resume the research from plan.json and run the next round of fetches.”

Requirements

  • Python, for plan.py, iterate.py and compile.py
  • Web fetching tools in the host agent

Workflow steps

3 steps, taken from the step headings in SKILL.md.

  1. Plan
  2. Iterate
  3. Compile

What it can do on your machine

Read from SKILL.md and the folder at commit 4494195. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 3 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Deep Research Workflow loads about 1.3k tokens when it runs, and up to ~3k if it reads all its reference files. Until then it costs about 180 tokens; SKILL.md has 467 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~180
When it runs · the whole SKILL.md, loaded when a task matches
~1.3k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from TokenRhythm/opensquilla at commit 4494195, republished under its Apache-2.0 licence (© TokenRhythm). 467 words, ~1,336 tokens.

Download SKILL.mdSave it as .claude/skills/deep-research/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.
name
deep-research
description
Multi-round research with explicit methodology, evidence tracking, and citation-tagged synthesis. Trigger on 'deep dive', 'research report', 'literature review', 'investigate X across sources', 'multi-round investigation'. Distinct from the `summarize` skill, which is a single-pass condensation; this skill maintains a state file across iterations, tracks coverage, and produces a long-form report with per-claim citations. Three execution stages: plan (scope into sub-questions), iterate (record evidence per round), compile (synthesize report). The skill itself does not fetch the web — it tells the host agent which fetches to perform via OpenSquilla's existing web tools, and records what comes back.
visibility
public
invocation
direct
description_zh
具有明确方法论、证据追踪和带引用标注综合的多轮研究。触发词如'深入研究'、'研究报告'、'文献综述'、'跨来源调查X'、'多轮调查'。区别于单轮浓缩的 summarize 技能:本技能跨迭代维护状态文件、追踪覆盖度,并生成带逐条引用的长篇报告,分为规划、迭代、汇编三个阶段。技能本身不抓取网页,而是通过OpenSqui…
provenance.origin
clawhub-mit0
provenance.license
MIT-0
provenance.upstream_url
https://clawhub.ai/in-depth-research
provenance.maintained_by
OpenSquilla

deep-research

Investigate a question by walking it through three explicit stages with a persisted state file. Use this when a single-pass summarize would lose too much, or when the user asks for a "research report" / "literature review". The host agent does the web fetching; this skill structures the work and keeps a paper trail.

Decide if this is the right tool

NeedUse
One-line summary of an articlesummarize
Multi-round investigation with citationsthis skill
Quick lookup, single sourcedirect web search
Continuous monitoring of a topica digest/cron skill

Stages

Scope → Plan → Iterate (×N) → Compile → Deliver

State persists in a single JSON file you pass between stages. The file is the contract; if you can describe the file, you can resume the research at any point.


Stage 1: Plan

bash
python {baseDir}/scripts/plan.py \
    --question "How did Manus differentiate from competing AI agents in 2025?" \
    --depth thorough \
    --out plan.json

--depth choices:

  • overview — 3-5 sub-questions, target 1 source per sub-question
  • thorough — 6-10 sub-questions, target 2-3 sources per sub-question
  • exhaustive — 12-20 sub-questions, target 5+ sources per sub-question

The plan is a pydantic model serialized to JSON; see references/methodology.md for the schema and the system-review approach the depth choices implement.


Stage 2: Iterate

Each round: read the plan, decide which sub-questions need attention, print the fetch list for the host agent to execute, and (after the agent returns results) record evidence back into the plan.

bash
# Show the host what to fetch this round
python {baseDir}/scripts/iterate.py --plan plan.json --round 1 --print-fetches

# After the host fetches, record results back
python {baseDir}/scripts/iterate.py --plan plan.json --round 1 \
    --record evidence_round_1.json

evidence_round_1.json:

json
[
  {
    "subquestion_id": "sq-002",
    "url": "https://...",
    "title": "...",
    "excerpt": "...",
    "relevance": 0.85,
    "fetched_at": "2026-05-06T10:14:00Z"
  }
]

The script updates per-sub-question coverage estimates. When all sub-questions reach the depth-target coverage, the plan's done flag flips to true and the iteration loop terminates.

See references/sources.md for the 5-axis source evaluation (Authority, Recency, Evidence, Bias, Corroboration) you should apply when judging relevance.


Show full SKILL.md (216 more words)Show less

Stage 3: Compile

bash
python {baseDir}/scripts/compile.py --plan plan.json --out report.md

Output is markdown with:

  1. Executive summary (5-8 lines)
  2. Methodology block (depth, rounds, source count)
  3. Per-sub-question section with embedded citations [^N]
  4. References block listing every source with URL + fetched_at + relevance
  5. "What this report does not cover" — explicit gaps from low-coverage sub-questions

Citations link to the references block. The compile step never invents sources — every [^N] in the body must correspond to an entry recorded in stage 2.


Boundaries

  • This skill does not fetch the web itself. It is a methodology + state manager. Pair it with the host agent's web search/fetch tools.
  • It does not resolve contradictions among sources automatically. The compile step will note conflicting evidence in the report; the user decides which side wins.
  • It is not a fact-checker. Source quality scoring is heuristic; treat the output as a starting point, not a verdict.
  • For ongoing monitoring (daily digests, RSS-style updates) build a cron skill that calls this one with a fresh question each cycle.

Differentiation from summarize

summarize takes one document and produces a shorter version. This skill takes one question and produces a researched report drawing on many documents, with explicit evidence tracking. They share no trigger words by design — summarize triggers on "summarize", "shorten", "tl;dr"; this skill triggers on "research", "investigate", "literature review", "deep dive".

© TokenRhythm, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 6 other files (scripts, references) in src/opensquilla/skills/bundled/deep-research of TokenRhythm/opensquilla.

  • SKILL.md
  • THIRD_PARTY_NOTICES.md
  • references/methodology.md
  • references/sources.md
  • scripts/compile.py
  • scripts/iterate.py
  • scripts/plan.py

Open the folder on GitHubat commit 4494195

Compare with similar skills

Deep Research Workflow next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Deep Research Workflow compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Deep Research Workflow this skillTokenRhythm/opensquilla7.1k—~1.3kAutomated safety check: PassApache-2.0
Academic Research Suite for CodexImbad0202/academic-research-skills-codex12k—~12kAutomated safety check: PassCustom licence
Deep Research Literature SurveyHKUSTDial/Supervisor-Skills8.4k—~2.4kAutomated safety check: PassCC-BY-NC-SA-4.0
Live Researchbrightdata/skills264—~1.8kAutomated safety check: PassMIT
Academic Researcheraiskillstore/marketplace4303 repos~2.1kAutomated safety check: PassMIT
Ulw Researchrlaope/oh-my-hermes3.2k—~4.2kAutomated safety check: PassMIT

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Questions about Deep Research Workflow

What does Deep Research Workflow do?

Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations. The skill structures an investigation as plan, iterate and compile, with all progress kept in one JSON state file that can resume the work at any point. It does not fetch the web itself: it prints a fetch list for the host agent to run with its own web tools and records the evidence that comes back.

When should I use Deep Research Workflow?

Deep Research Workflow fits situations like: producing a research report with a citation for each claim; running a multi-round literature review that can be resumed; scoping a broad question into sub-questions and tracking coverage.

How do I install Deep Research Workflow in Claude Code?

Run `npx skills add TokenRhythm/opensquilla --skill deep-research -a claude-code`. Or copy the skill folder (src/opensquilla/skills/bundled/deep-research in TokenRhythm/opensquilla) into .claude/skills/deep-research in your project. Claude Code loads it when a task matches its description.

How do I install Deep Research Workflow in Codex?

Run `npx skills add TokenRhythm/opensquilla --skill deep-research -a codex`. Or copy the skill folder (src/opensquilla/skills/bundled/deep-research in TokenRhythm/opensquilla) into .agents/skills/deep-research in your project. Codex loads it when a task matches its description.

Can I use Deep Research Workflow in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add TokenRhythm/opensquilla --skill deep-research -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/deep-research, .gemini/skills/deep-research, .github/skills/deep-research and .opencode/skills/deep-research in your project.

What does Deep Research Workflow need to run?

Going by SKILL.md and its folder, Deep Research Workflow needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python, for plan.py, iterate.py and compile.py; Web fetching tools in the host agent.

Does Deep Research Workflow access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Deep Research Workflow safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Deep Research Workflow use?

Deep Research Workflow is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Deep Research Workflow use?

About 1.3k tokens (SKILL.md is roughly 5.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.6k tokens, read only when the agent opens those files.

What are the alternatives to Deep Research Workflow?

Skills that share tags, products or a category with Deep Research Workflow: Academic Research Suite for Codex (Imbad0202/academic-research-skills-codex, 12k stars), Deep Research Literature Survey (HKUSTDial/Supervisor-Skills, 8.4k stars), Live Research (brightdata/skills, 264 stars) and Academic Researcher (aiskillstore/marketplace, 430 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Deep Research Workflow?

TokenRhythm (a GitHub organization) maintains it in TokenRhythm/opensquilla, which has 7,087 GitHub stars. The repository holds 8 skills in this directory. The repository was last updated on October 4, 2026.

Source: TokenRhythm/opensquilla on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.