bio-tools-execution-playbook

name	bio-tools-execution-playbook
description	Execution playbook for bio_tools remote mode, with reusable request templates and I/O conventions. Trigger when agent needs concrete payloads for tool_name/operation/params.

Bio Tools Execution Playbook

Workflow

1. Start from references/request_templates.json.
2. If template missing, call help and derive minimal params.
3. Execute with bio_tools in remote mode and inspect metadata (run_id, remote_run_dir, local_artifact_dir).
4. Chain dependent operations only after verifying required artifacts exist locally.

I/O conventions

• Inputs: absolute local paths preferred.
• Outputs: short relative names.
• Reuse local_artifact_dir outputs for dependent calls when possible.

Canonical chains

• makeblastdb -> blastn/blastp
• bwa index -> bwa mem
• samtools view -> sort -> stats

Reference

• Templates: references/request_templates.json