add documentation for sunbeam

Closes #8 (closed)

simulation/README.md

@@ -24,6 +24,9 @@ make the process a bit faster. Files can be found in the `example/` directory.
 All the path are preceded by the `/input` directory since we are going to mount our config
 files into this directory.
 
+> **Warning** Generated paired-end reads are in one unique `fastq` file that need to be
+splitted in `_R1` and `_R2` files.
+
 ### With docker
 
 ```bash
@@ -71,13 +74,10 @@ output_directory=out
 temp_directory=/tmp
 gsa=True                # whether a gold standard assembly should be created
 pooled_gsa=True         # whether a pooled gold standard over all samples is created
-anonymous=False         # whether the output is anonymized
+anonymous=True          # whether the output is anonymized (reads from genomes are shuffled)
 compress=1              # 0 is for no compression, 9 is maximum compression
 ```
 
-Since we do not need the data for a challenge, we can switch off the anonymous part of the process. _For the moment it seems that it [does not work without anonymization]
-(https://github.com/CAMI-challenge/CAMISIM/issues/64) so it is better to keep the `anonymous` flag to `True`_.
-
 #### Read Simulator
 
 ```ini