The shuffle node is probably one of the most confusing in Nuke, and it looks like a mess at first. But there's a logic behind all these littles squares and arrows. 

Input on the top, output on the right.

Starting on the upper left: "in1" is your input. That's what comes in the node. Under that you have arrows pointing down. If you follow the arrow under "r" you'll encounter a checkmark right away. After that checkmark, go right all the way and there's your output. That's what will come out of the Shuffle node for that channel. The same logic applies for the other channels. By default, the node outputs the red channel to red, green to green, etc. As a result, it's not changing anything. 

The input red channel outputs to red AND alpha channel since they're both checked.

Let's say your elements doesn't have an alpha channel like the smoke element in this example. Under the "r" column, check the last red box, and if you follow right you can see it output as alpha. You now successfully shuffle the red channel in the alpha channel. 

If you decided to only keep the blue channel, you can select all the boxes under the blue ("b" column) and the will shuffle blue to all the other channels. If you take a look at the different channels in the viewer you'll see they're now all the same. 

That's one use for the shuffle. But where it gets really useful is when working with CG elements and multi-pass EXR files. 

By selecting the specular pass in the input dropdown menu (upper left) we're shuffling it to the rgba output. (right)

By selecting the specular pass in the input dropdown menu (upper left) we're shuffling it to the rgba output. (right)

Looking at a CG render through a LayerContactSheet node, you can see a number all the passes contained in that file. Let's say you want bring the specular pass to rgba where you can see it. With a new shuffle node, go to the "in1" dropdown menu and select specular. That will shuffle the RGB channels of the specular pass to the RGB channels of the viewer and the specular pass is now the output of the shuffle node. 


Since a specular pass doesn't have an alpha pass, the shuffle copied the blue channel into alpha. That gives you an alpha that doesn't make much sense. But If you click on the black box instead, you're alpha will be fully black, the white box will give you a fully white alpha. 

Now the output has the specular pass in the RGB channels but keeps the original alpha.

But what would make more sense is to have the specular pass in RGB but keep the original alpha channel. You can do that by going to the dropdown menu of "in2" and select RGBA or alpha. And check the mark to output the alpha channel of in2 to the node's output. This way you can mix different channels into a new one. 

When using a shuffle, in our case the specular pass overrides the original RGB channels so keep in mind that those channels are lost after the shuffle node. 

Shuffle node is definitely a node that's used all the time with CG elements and it's a very useful feature of Nuke