leaf watch

Real-time folder monitoring runs targeted extraction as new .raw, .mzml, or .mzml.gz files arrive in a folder. This is useful on acquisition computers where samples are written continuously.

Synopsis

leaf watch run    FOLDER [OPTIONS]   # foreground
leaf watch start  FOLDER [OPTIONS]   # detached daemon
leaf watch stop                       # terminate the daemon
leaf watch status                     # show daemon state

Required argument

Argument	Description
FOLDER	Folder to monitor for new .raw, .mzml, or .mzml.gz files

Common flags

Flag	Default	Description
--list-path PATH	(auto-discovered if omitted)	Compound list CSV — same schema as leaf targeted.
-o, --output PATH	(sibling of FOLDER)	Where to write per-file .msd archives.
--polarity {NEG,POS}	NEG	MS polarity.
--tolerance INT	5	m/z tolerance in ppm.
--rt-window FLOAT	0.3	Retention-time search window.
--idle-timeout FLOAT	60	Stop watching after N minutes with no new files.
--poll-interval FLOAT	10	Seconds between filesystem polls.
--stability-time FLOAT	10	Wait N seconds after a file stops growing before processing (avoids partial reads).
--multi / --no-multi	off	Watch multiple sub-folders concurrently.

For the full flag set, run leaf watch run --help.

Recipe — foreground watch

leaf watch run /path/to/inbox --list-path ./compounds.csv -o /path/to/outputs

Stops with Ctrl+C.

Recipe — daemon

leaf watch start /path/to/inbox --list-path ./compounds.csv -o /path/to/outputs
leaf watch status
leaf watch stop

The daemon survives terminal close. Use leaf watch status to verify it is running and to see the last-processed file.

Legacy shim

leaf-watch is a console-script shim equivalent to leaf watch run.

Next

→ leaf targeted — same extraction pipeline, one-shot