I am using http://www.patchwork-synth.com Is there any way to save the output in a file? I haven't found anything yet. Any help would be much appreciated.
Just having a little play around on that it seems like you can't, but there are ways around this... if you had your patchwork playing on a laptop, and had a pc laying around, you could connect the sound output of your Laptop in to the sound input of your Desktop and record it through a DAW, or you could just use a screen recorder that captures sound too, and play the track whilst recording, and use some video editing software to cut the video out and just leave and export it as audio.
You don't say which platform you are on, but in OSX you could use Soundflower to route to an audio recording program. Jack may work for Windows too.