How do I resume a run, or rerun everything from scratch?

run_together and the individual CartLoader commands plan their work as a Makefile, so:

• Resume: rerun the same command. Steps whose outputs already exist are skipped, so an interrupted or failed run continues from where it stopped.
• Rerun everything: add --restart, which rebuilds every step (make -B).
• Preview: add --dry-run to write the Makefile and print the planned commands without executing them.

With run_together

# Resume after an interruption: the same command again
cartloader run_together --platform 10x_xenium --in-dir IN --out-dir OUT --id my_sample

# Run or skip particular stages (stages outside the selection are assumed done)
cartloader run_together ... --only ingest,ficture
cartloader run_together ... --skip images

# Rebuild everything
cartloader run_together ... --restart

Changing a setting such as --n-factor or --width adds new models alongside the existing ones on the next run. --restart is only needed to redo steps whose outputs already exist.

With the individual commands

cartloader run_ficture2 ... --dry-run     # inspect commands only
cartloader run_ficture2 ... --restart     # force a full rerun

See also:

• run_together reference
• FICTURE Analysis reference