I use this pattern for CMake shaders that works with both Ninja and the MSVC generators.
# Build HLSL shaders
add_custom_target(shaders)
set(HLSL_SHADER_FILES VertexShader.hlsl PixelShader.hlsl)
set_source_files_properties(VertexShader.hlsl PROPERTIES ShaderType "vs")
set_source_files_properties(PixelShader.hlsl PROPERTIES ShaderType "ps")
set_source_files_properties(${HLSL_SHADER_FILES} PROPERTIES ShaderModel "4_0")
foreach(FILE ${HLSL_SHADER_FILES})
get_filename_component(FILE_WE ${FILE} NAME_WE)
get_source_file_property(shadertype ${FILE} ShaderType)
get_source_file_property(shadermodel ${FILE} ShaderModel)
add_custom_command(TARGET shaders
COMMAND fxc.exe /nologo /Emain /T${shadertype}_${shadermodel} $<IF:$<CONFIG:DEBUG>,/Od,/O1> /Zi /Fo ${CMAKE_BINARY_DIR}/${FILE_WE}.cso /Fd ${CMAKE_BINARY_DIR}/${FILE_WE}.pdb ${FILE}
MAIN_DEPENDENCY ${FILE}
COMMENT "HLSL ${FILE}"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
VERBATIM)
endforeach(FILE)
...
add_dependencies(${PROJECT_NAME} shaders)
I use this in my DirectX Tool Kit tutorials. You can also see the rest of the CMake on directx-vs-templates.