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CLI Reference

Commands

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

GUI Reference
GUI Reference
CLI Reference
neuropipe run