For a full run (preproc with GFS init + model run),

./gfs_fullrun.sh

runs gfs_pre00_init_atmosphere.sh -> gfs_run_mpas.sh

For just pre-proc,

./gfs_pre00_init_atmosphere.sh

runs gfs_pre01_download.sh -> gfs_pre02_ungrib.sh -> gfs_pre03_init_conds.sh -> gfs_pre04_lbc.sh

For just the model run (assuming you already have preproc'd files),

./gfs_run_mpas.sh

A lot of this code is adapted from UGA-WRF preproc/download scripts.