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name: pipelines-integrations description: "Operate ClawBio's optional MCP stdio server, messaging and web adapters, provider bridges, and nf-core Nextflow wrappers with explicit safety, credential, network, and preflight boundaries." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Pipelines and Integrations

Use this sub-skill for integrations around ClawBio rather than for the scientific interpretation itself. It covers the optional MCP server, RoboTerri Telegram/Discord/WhatsApp adapters, Robotary/OpenClaw web routes, the FLock provider bridge, and the scrnaseq-pipeline, rnaseq-pipeline, and sarek-pipeline wrappers.

Route

• MCP discovery, stdio setup, demo-only defaults, or local-file opt-in: read references/integrations.md.
• Telegram, Discord, WhatsApp, Robotary, OpenClaw webchat, provider credentials, file handling, or structured chat follow-up: read references/integrations.md.
• Any nf-core/Nextflow command, profile, reference, resume, --check, network, container, or large-data question: read references/pipeline-preflight.md.
• A missing optional dependency, credential, binary, stale resume, rejected input, or failed handoff: read references/troubleshooting.md.
• For ordinary ClawBio skill execution, output inspection, or reproducibility bundles, hand off to core-runner.

Operating procedure

1. Establish the boundary before acting: package importability is not service readiness; an installed optional module is not proof that credentials, network access, a webhook, a gateway, Nextflow, a container backend, or references are usable.
2. Prefer safe, non-starting diagnostics with scripts/check_integrations.py. Run its --help first when unfamiliar. It only probes imports and executable availability, and an optional CLI help probe; it never starts a bot, MCP transport, web server, or Nextflow run.
3. For MCP, use clawbio mcp over stdio. Keep the default demo-only policy; local input/output access requires an explicit operator environment opt-in. Do not place secrets or patient paths in a client configuration.
4. For bots and web adapters, collect only the platform/provider settings required for the chosen adapter, keep identities and received files scoped to the sender/session, and treat platform APIs and external LLMs as network boundaries. Never echo or log credentials.
5. For a pipeline, choose one exact wrapper command, a fresh output directory, an explicit backend/profile and reference strategy, then run --check before a real run. Use only flags documented in the wrapper contract or the ClawBio registry allowlist; do not invent Nextflow parameters.
6. Preserve the wrapper's preflight decisions. Do not bypass local-first remote input checks, config trust checks, output-location checks, version pins, or resume incompatibility errors. Long runs and large references need an explicit disk/network/container budget.
7. After execution, inspect result.json, report.md, logs, and any preferred artifact before offering a follow-up. Pass confirmed artifacts to the relevant core/domain skill; do not infer a handoff from an exit code alone.

Safety boundary

• Do not run live credentials, network calls, long pipelines, containers, or large reference/model/data downloads while drafting or diagnosing this sub-skill.
• MCP demo execution is the safe default. CLAWBIO_MCP_ALLOW_LOCAL_FILES=1 is a deliberate exception that can expose local genomic data and outputs.
• Messaging adapters necessarily contact their platform and configured LLM; that is distinct from ClawBio's local computation guarantee. WhatsApp webhook requests fail closed without a valid app-secret signature, and public sender access must be explicit.
• Nextflow configs are trusted Groovy code, not a sandbox. Remote inputs, iGenomes, containers, conda environments, Wave, and object-store work dirs can require network access and substantial storage.
• Keep ClawBio's research/educational disclaimer and direct medical questions within the domain skill's safety contract.

Handoff contract

A successful integration run returns a structured result or an adapter-visible bundle. Use result.json fields such as workflow_state, chat_summary_lines, preferred_artifacts, suggested_actions, and contract_alerts when present. An action offer is a stored structured request, not fresh shell text: execute it only through the normal runner path. Pipeline wrappers commonly expose a confirmed preferred_h5ad, preferred_counts_tsv, VCF inventory, or downstream command template. Point ordinary output interpretation to core-runner and scientific follow-up to the named domain skill.