Doc commands have incorrect syntax

The doc command blocks aren't copy-and-pasteable due to extraneous `$` symbols, e.g.

To run locally, we invoke the following command:
```
$ bdg-deca \
$   --targets <regions> \
$   --samples <manifest> \
$   --output-dir <path-to-save> \
$   --memory <memory-in-GB> \
$   --run-local \
$   file:<toil-jobstore-path>
```
