How can you add an effect file on the Monogame pipe line?
was planning to do some simple shaders using GLSL
There is no support for GLSL yet, but it is planned. There are some hurdles to overcome and some steps have been made towards it, but it is not there yet.
Surely there is support for GLSL with the rendering outputs of MonoGame that support it? For instance the OpenGL Windows desktop project.
I should clarify that there is no support yet for directly importing a GLSL file. For OpenGL platforms, we import a .fx file containing HLSL, which is converted to GLSL by a library called MojoShader. This process may seem complex, but it gives us the metadata we need to support the shader. GLSL is compiled in the application by the OpenGL driver to an internal format that we cannot parse.
The plan is to support GLSL in a .fx file so we can parse the .fx file to get the metadata we need and pass the GLSL through to the .xnb file, as discussed in this issue on GitHub.