Run

Start a pipeline run, wait for completion, and download results. Prefer --input for full payloads; top-level flags remain available as overrides.

This is CLI workflow behavior, not a standalone REST endpoint. It composes generated API commands from this resource to submit work, wait for completion, and persist local results.

boltz-api small-molecule:design run

Options

Option	Description
--input [ --input ]	Structured request input. Merges fields into the top-level request body. Prefer —input for complete structured payloads or @json://... files. Top-level body flags can still override individual fields. Keep --idempotency-key and --workspace-id top-level; if also present in --input, the top-level flag wins.
--num-molecules	Number of molecules to generate. Must be between 10 and 1,000,000. You can set this directly, or prefer —input for the full payload. If both are set, this flag overrides the matching field from --input.
--target [ --target ]	Target protein sequences for small molecule design or screening. You can set this directly, or prefer —input for the full payload. If both are set, this flag overrides the matching field from --input.
--chemical-space	Chemical space to constrain generated molecules. Currently only ‘enamine_real’ (Enamine REAL chemical space) is supported. Additional options may be added in the future. You can set this directly, or prefer —input for the full payload. If both are set, this flag overrides the matching field from --input.
--idempotency-key	Client-provided key to prevent duplicate submissions on retries. Keep this as a top-level flag even when using —input. If also present in --input, this top-level flag wins.
--molecule-filters [ --molecule-filters ]	Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. You can set this directly, or prefer —input for the full payload. If both are set, this flag overrides the matching field from --input.
--workspace-id	Target workspace ID (admin keys only; ignored for workspace keys). Keep this as a top-level flag even when using —input. If also present in --input, this top-level flag wins.
--name string	Local run directory name under —root-dir
--run-dir string	Explicit local run directory path
--root-dir string	Root directory for generated local run directories (default: “boltz-experiments”)
--poll-interval-seconds float	Polling interval while waiting for remote results (default: 5)
--progress-format jsonl	Format for progress logs written to stderr (jsonl or text). jsonl is the default agent-friendly format. (default: “jsonl”)
--verbose, -v	Print text progress logs to stderr when —progress-format text is selected (default: false)
--download-mode everything	Pipeline artifact download mode (everything or metadata_only). (default: “everything”)
--workers int, --num-workers int, --num_workers int	Number of concurrent pipeline result archive downloads (default: 32)
--help, -h	show help