Update README.md

README.md

@@ -43,12 +43,14 @@ verbose as possible — e.g. include the command line, etc
 Quickstart
 
 1. open a shell
-2. make a folder, name it yourself, I named it workdir 
+2. make a folder, name it yourself, I named it workdir
+
 ```
 mkdir workdir
 cd workdir
 ```
 2. clone the project and switch to the main folder, it's your working directory
+
 ```
 git clone http://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools.git
 cd snakemake_only_obitools
@@ -57,6 +59,7 @@ cd snakemake_only_obitools
     - folder which contains reference database files. You can built a reference database by following the instructions [here](projet_builtdatabase).
     - folder which contains pairend-end raw reads `.fastq.gz` files and the sample description `.dat` files. Raw reads files from the same pair must be named as `*_R1.fastq.gz` and `*_R2.fastq.gz` where wildcard `*` is the name of the sequencing run. The alphanumeric order of the names of sample description `.dat` files must be the same than the names of paired-end raw reads `.fastq.gz` files. The sample description file is a text file where each line describes one sample. Columns are separated by space or tab characters. Sample description file is described [here](https://pythonhosted.org/OBITools/scripts/ngsfilter.html).
 4. run the pipeline :
+
 ```
 bash main.sh /path/to/fastq_dat_files /path/to/reference_database_folder 16
 ```