Reference.md

@@ -40,8 +40,12 @@ Output and input can take any values. We defined them as wildcards. We use 4 wil
 
 # Rules
 
+A Snakemake workflow is defined by specifying rules in a Snakefile. Rules decompose the workflow into small steps by specifying how to create sets of output files from sets of input files.
+
 ## Overview
 
+Snakefile in green, output files in yellow, configuration files in white, rules in grey.
+
 ```mermaid
 
 graph TD;