This can all be done by operators (except the pixel geocoding)
Please have a look at this post:
For subetting there is the ‘Subset’ operator and for reprojection you use the ‘Reproject’ operator.
Saving as NetCDF4 can be done with the ‘Write’ operator.
You can also get the parameters names when you invoke the gpt from the command line:
gpt Subset -h
This will show the help for the Subset operator.
As output format for the Write operator you should use ‘NetCDF4-CF’