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run-yaml-workflow

Run one or more fp-tools jobs from a reusable YAML configuration.

Example command

run-yaml-workflow --config examples/gui_configs/diff_footprints_single.yml

Primary inputs

  • --config — command-compatible YAML configuration exported by the GUI or written directly.

Main outputs

  • The exact files documented for each command named in the YAML; YAML does not create a separate analysis format.
  • Standard output containing the expanded command lines when --dry-run is used.
  • {run_root}/{job_id}/config.yml and command.txt — normalized per-job configuration and exact command.
  • {run_root}/{job_id}/status.json, stdout.log, and stderr.log — completion state and captured command output.
  • {run_root}/batch_index.tsv — one-row-per-job batch status index.

Paths are resolved according to the YAML runner and remain independent of GUI state. Inspect the dry-run expansion before starting a long workflow.

The YAML remains command-compatible and does not require GUI state. See the complete run-yaml-workflow reference.