Update README.md

README.md

@@ -44,17 +44,23 @@ Quickstart
 
 1. open a shell
 2. make a folder, name it yourself, I named it workdir 
-    `mkdir workdir`
-    `cd 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`
+```
+git clone http://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools.git
+cd snakemake_only_obitools
+```
 3. define 2 folders : 
     - 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`
-    - order of arguments is important : 1) path to the folder which contains paired-end raw reads files and sample description file 2) path to the folder which contains reference database files 3) number of available cores (here for instance 16 cores)
+```
+bash main.sh /path/to/fastq_dat_files /path/to/reference_database_folder 16
+```
+order of arguments is important : 1) path to the folder which contains paired-end raw reads files and sample description file 2) path to the folder which contains reference database files 3) number of available cores (here for instance 16 cores)
 5. run the pipeline step by step :
 open the file `main.sh` to see details