Update README.md

README.md

@@ -14,12 +14,10 @@ This was designed to process RADseq data from [RESERVEBENEFIT](https://www.biodi
   3. [Set up](#23-set-up)
 3. [Reporting bugs](#4-reporting-bugs)
 4. [Running the pipeline](#5-running-the-pipeline)
-  1. [Filter raw data](#51-filter-raw-data)
-  2. [Georeferenced sequences alignments by species](#52-data-files)
-  3. [Species sequence pairwise comparison](#53-species-sequence-pairwise-comparison)
-  4. [Genetic Diversity calculation](#54-genetic-diversity-calculation)
-  5. [Statistical analysis](#55-statistical-analysis)
-
+  1. [Initialisation](#41-initialisation)
+  2. [Configuration](#42-configuration)
+  3. [Run the pipeline into a single command](#43-run-the-pipeline-into-a-single-command)
+  4. [Run the pipeline step by step](#44-run-the-pipeline-step-by-step)
 
 
 # 1. Introduction
@@ -131,7 +129,7 @@ verbose as possible — e.g. include the command line, etc
 
 # 4. Running the pipeline
 
-Quickstart
+## 4.1 Initialisation
 
 * open a shell
 * make a folder, name it yourself, I named it workdir
@@ -146,9 +144,24 @@ cd workdir
 git clone http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2.git
 cd snakemake_stacks2
 ```
+## 4.2 Configuration
+WORK IN PROGRESS !!!!
+
+## 4.3 Run the pipeline into a single command
+One you finished [Initialisation](#41-initialisation)) and [Configuration](#42-configuration) steps. You can run the whole pipeline simply typing :
+```
+## number of CPU cores available for running the pipeline (for instance here 64 cores)
+N_CORES=64
+## run the pipeline into a single command
+bash main.sh $CORES
+```
 
 
+## 4.4 Run the pipeline step by step
 WORK IN PROGRESS !!!!
 
 that's it ! The pipeline is running and crunching your data. Look for the log folder output folder after the pipeline is finished.
 
+
+
+