Document me :-)

docs/configuration/reference_genomes.md

@@ -10,7 +10,6 @@ Read [Adding your own system](adding_your_own.md) to find out how to set up cust
 ## Adding paths to a config file
 Specifying long paths every time you run the pipeline is a pain.
 To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline.
->>>>>>> TEMPLATE
 
 Note that this genome key can also be specified in a config file if you always use the same genome.
 

docs/usage.md

@@ -136,7 +136,7 @@ If you prefer, you can specify the full path to your reference genome when you r
 ```bash
 --fasta '[path to Fasta reference]'
 ```
-> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`.
+> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`. You may also specify the path to a gzipped (`*.gz` file extension) FastA as reference genome - this will be uncompressed by the pipeline automatically for you.
 
 ### `--genome` (using iGenomes)