Alterlab Workflow Orchestration

Workflow Orchestration — Compose AlterLab Skills into Multi-Agent Workflows

This skill is the orchestration layer. It does not do research, write, or review itself — it teaches how to wire the skills that do into agentic workflows using Claude Code's native subagent machinery and the Claude Agent SDK. Pick a pattern, point it at real AlterLab skills, copy the delegation prompt.

The five patterns below are the high-leverage shapes for academic work: fan-out parallel investigation, a sequential pipeline, a judge panel, adversarial verification, and a loop-until-clean review cycle. Each is grounded in the current docs (see references/claude-orchestration-primitives.md for the verified primitives, and references/composition-recipes.md for full worked recipes with copyable prompts).

When to Use This Skill

Use this skill when the user wants to:

• Run several AlterLab skills at once over independent inputs (e.g. verify 4 bibliographies, or research 3 sub-questions in parallel) and merge the results
• Chain skills into a pipeline where each stage hands off to the next
• Get multiple independent perspectives on one artifact (a judge / reviewer panel)
• Adversarially verify an output — one agent produces, a fresh agent tries to break it
• Iterate a loop until a quality gate passes (e.g. re-review until zero unresolved comments)
• Understand Claude Code subagents, agent teams, forks, or the Agent SDK well enough to author their own academic orchestration

Does NOT Trigger

This skill is for how to compose; the named skills are what to compose. If a single existing skill already does the job end to end, defer to it.

Verified Orchestration Primitives (Claude Code + Agent SDK)

Verified against code.claude.com/docs on 2026-09-23 (Claude Code v2.1.280). See references/claude-orchestration-primitives.md for quotes, field tables, and version gates.

• Subagents are Markdown + YAML files in .claude/agents/ (project), ~/.claude/agents/ (user), or a plugin's agents. Only name and description are required; the tool allowlist field is tools (comma-separated or a YAML list), and model accepts sonnet/opus/haiku/fable/a full ID/inherit. Each subagent runs in its own context window and returns only a summary. Claude auto-delegates by matching the task to the description.
• Subagents can nest — by default up to three layers below the main conversation (CLAUDE_CODE_MAX_SUBAGENT_SPAWN_DEPTH; 1 turns nesting off). A reviewer can dispatch one verifier per finding. Omit Agent from a subagent's tools to keep it from spawning. Built-ins: Explore and Plan (read-only, inherit the main model), general-purpose (all tools).
• Fork mode is on by default in interactive sessions: Claude can spawn a fork that inherits the whole conversation (and its prompt cache), and subagents run in the background. Start one yourself with /subtask.
• Dynamic workflows move the plan into a JavaScript script the runtime executes: agent(), parallel(), pipeline(), phase(), args, with JSON-schema outputs and intermediate results kept in script variables instead of Claude's context. Dozens to hundreds of agents per run; resumable; saved to .claude/workflows/ or shipped in a plugin's workflows/ folder and run as /<name> or /<plugin>:<name>.
• Agent teams (experimental, CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1, interactive sessions only): teammates have independent contexts, a shared task list, and message each other directly — the right tool for sustained adversarial debate. Higher token cost.
• Claude Agent SDK (Python claude-agent-sdk, TypeScript @anthropic-ai/claude-agent-sdk) packages the same agent loop programmatically via query(...); define subagents with the agents option (AgentDefinition) and resume by session_id. Use it to script the patterns below in CI or batch jobs.

Ready-made versions. The alterlab-workflows plugin ships these patterns as runnable dynamic workflows (documented in alterlab-research-workflows): fan-out + adversarial verify → citation-audit; judge panel → review-panel and grant-mock-panel; adversarial verification → claim-stress-test; dual independent coding with adjudication → systematic-review-screening. Adapt one of those before writing a new workflow from scratch.

The Five Patterns

1. Parallel fan-out (map)

When N inputs are independent, dispatch one worker per input and merge. Classic academic uses: verify several bibliographies at once, or research distinct sub-questions concurrently.

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I have 4 reference lists (one per chapter). Verify them in parallel using
separate subagents — each subagent runs the alterlab-citation-verifier skill
on one list — then merge the per-entry verdicts into one table flagging every
TF/IH/SH problem across all four chapters.

Why subagents: each verification floods context with API lookups you won't reuse; isolating each in its own window keeps the main conversation clean. Best when paths don't depend on each other (the docs' stated condition for parallel research). See recipe P1 in references/composition-recipes.md.

2. Sequential pipeline (chain)

Stage outputs feed the next stage. The canonical academic chain — research → write → integrity-check → review → revise — is already packaged as alterlab-research-pipeline; prefer that skill rather than rebuilding it. Use this pattern when you need a custom chain it doesn't cover, e.g. deep-research → citation-verifier → peer-review on an externally supplied draft.

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Use the alterlab-deep-research skill to produce a lit-review synthesis on X,
then chain its bibliography into alterlab-citation-verifier to existence-check
every entry, then pass the verified draft to alterlab-peer-review for a
section-by-section critique. Carry forward only each stage's summary.

See recipe P2 in references/composition-recipes.md.

3. Judge panel (independent multi-perspective)

Several independent reviewers each apply a different lens to one artifact, then a synthesizer reconciles. alterlab-paper-reviewer already simulates a 5-reviewer panel internally; use this pattern when you want the panelists to be genuinely separate agents (separate contexts, no cross-contamination) — e.g. a methodology reviewer, a domain reviewer, and a reproducibility reviewer that must not anchor on each other.

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Spawn three independent reviewer subagents on this manuscript: one on
methodology, one on domain contribution, one on reproducibility/statistics.
Each works from the paper alone and reports independently; then synthesize a
single editorial decision noting where they agree and disagree.

Independence is the point — running them in one context lets the first opinion anchor the rest. See recipe P3 in references/composition-recipes.md.

4. Adversarial verification (produce → break)

One agent produces a claim or result; a fresh agent is tasked solely with disproving it. This is the highest-value pattern for research integrity. The docs' competing-hypotheses agent-team example is the reference implementation: teammates "talk to each other to try to disprove each other's theories, like a scientific debate."

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Take the three headline claims in my draft. For each, spawn a skeptic subagent
whose only job is to find disconfirming evidence and check the supporting
citation actually supports the claim (via alterlab-citation-verifier). Report
any claim that survives and any that breaks.

For sustained debate where the skeptics challenge each other, escalate to an agent team (the env var above). See recipe P4 in references/composition-recipes.md.

5. Loop until clean (validator → fix → repeat)

Iterate a fix-and-recheck cycle until a quality gate passes — bounded by a turn cap so it terminates. Academic use: revise → re-review until zero unresolved reviewer comments, or verify → fix → re-verify until the bibliography is 100% resolvable.

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Run a revision loop: alterlab-paper-reviewer produces comments; revise the
draft to address them; re-review only the previously-flagged items; repeat
until no unresolved comments remain or after at most 3 rounds, then stop and
report the residual issues.

Always set an explicit stop condition and a max-iteration cap — open loops burn context and tokens. As a dynamic workflow, the loop lives in the script:

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export const meta = { name: 'revise-until-clean', description: 'Review, revise, re-review until no unresolved comments or 3 rounds' }
let open = []
for (let round = 1; round <= 3; round++) {
  const review = await agent(`Review draft.md (round ${round}); list unresolved comments only.`,
    { schema: { type: 'object', required: ['comments'], properties: { comments: { type: 'array', items: { type: 'string' } } } } })
  if (!review) break          // agent() returns null if the run is stopped or the agent fails
  open = review.comments
  if (!open.length) break
  await agent(`Revise draft.md to resolve exactly these comments: ${JSON.stringify(open)}`)
}
return { unresolved: open }

See recipe P5 in references/composition-recipes.md.

Choosing a Mechanism

Match freedom to fragility: open-ended exploration gets prose prompts; fragile multi-step sequences get explicit, ordered instructions and a stop condition.

Resources

• references/claude-orchestration-primitives.md — verified Claude Code subagent
  • agent-team + fork + Agent SDK primitives, with field tables and doc-sourced quotes (load when you need exact frontmatter fields, env vars, or version gates)
• references/composition-recipes.md — five full worked recipes (P1–P5) mapping each pattern onto real AlterLab skills, with copyable delegation prompts, subagent-definition frontmatter, and a Python Agent SDK query() example (load when you need a complete, ready-to-run composition)