In one of my projects, configured with CMake, I can see that the reulting build.ninja has lines like this (emphasis mine):

build CMakeFiles/package.util: CUSTOM_COMMAND all
  COMMAND = cd /home/abertulli/<project_root>/<build_directory> && /usr/bin/cpack --config ./CPackConfig.cmake
  DESC = Run CPack packaging tool...    ## <-- NOTE HERE
  pool = console
  restat = 1

Pheraps this does what you'd like?