Example request for an AI agent

Copy and adapt the text below when starting a new analysis.

Read AGENTS.md, agent/README.md, agent/workflow_contract.yaml, and the relevant tutorial chapters. Work in new_study_dry_run mode. My sample registry is config/local/my_samples.tsv, my parameters are config/local/my_analysis_parameters.json, and my status file is agent/local_status/my_analysis_status.json. Validate the configuration without modifying raw or reference inputs and without running biological computation. Report structural errors, warnings, unresolved scientific decisions, and the next single stage that could be approved. Do not guess missing values or advance past a human-approval gate.

After reviewing the dry run, authorize one stage explicitly and name its output directory. An instruction such as “continue the whole workflow” should not be treated as approval to bypass unresolved decisions or failed validation gates.