You can use this script with the following example:
  Rscript inst/scripts/prepare_libraries_sop_closed.R --fil-lib-sop-raw-clo ../lotus-processor/data/processed/220226_closed_metadata.csv.gz --fil-lib-sop-pre data/interim/libraries/sop/closed_prepared.tsv.gz

Usage:
  prepare_libraries_sop_closed.R [--fil-lib-sop-raw-clo=<fil-lib-sop-raw-clo>] [--fil-lib-sop-pre=<fil-lib-sop-pre>]

Arguments:
  fil-lib-sop-raw-clo        Closed raw structure organism pairs library. STRING
  fil-lib-sop-pre            List of prepared structure organism pairs libraries. STRING

Options:
  -h --help                  Shows this screen.
  -v --version               Shows version.