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CLI Reference

Commands

CommandDescription
neuromaestro runSubmit pipeline jobs to SLURM
neuromaestro initInitialise a new project directory with config and script templates
neuromaestro check-outputsInspect which subjects completed a task
neuromaestro detect-subjectsFind subject IDs in a directory
neuromaestro list-tasksList all configured tasks
neuromaestro generate-configGenerate a blank project config template
neuromaestro generate-checksGenerate a blank results-check config template
neuromaestro merge-logsManually merge JSONL logs into the SQLite database
neuromaestro force-rebuildRebuild a fresh database from all JSONL logs, including archived
neuromaestro generate-reportGenerate a standalone HTML report from the job database
neuromaestro-guiLaunch the web-based GUI
neuromaestro run

All flags for submitting pipeline jobs — subjects, stages, dry-run, resume, wait.

Database Commands

check-outputs, merge-logs, force-rebuild, generate-report, and the database schema.

Utility Commands

detect-subjects, list-tasks, neuromaestro-gui, generate-config, generate-checks.

GUI Reference
GUI Reference
CLI Reference
neuromaestro run