update readme

README.md

-# RNAflow
+<img align="left" width="100" height="100" src="images/RNAflow_logo.png" alt="RNAflow">
 
-[![Snakemake](https://img.shields.io/badge/snakemake-≥5.2.1-brightgreen.svg)](https://snakemake.readthedocs.io/en/stable/) [![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)
+# RNAflow: A snakemake-based pipeline for standard transcriptmic analysis
 
+[![Snakemake](https://img.shields.io/badge/snakemake-≥5.2.1-brightgreen.svg)](https://snakemake.readthedocs.io/en/stable/) [![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)
 
+## Table of content
 
-## Authors
-
-* Rachel Legendre (@rlegendr)
+[[_TOC_]] 
 
-## Contributors
-
-* Adrien Pain
-* Claudia Chica
-* Elise Jacquemet
-* Emeline Perthame
-* Emmanuelle Permal
-* Hélène Lopez-Maestre
-* Hugo Varet
-* Natalia Pietrosemoli
-* Victoire Baillet
-* Vincent Guillemot
 
-## What is RNAflow ?
+# What is RNAflow ?
 
 RNAflow is a snakemake pipeline dedicated to standard transcriptomic analysis [@Hub of Bioinformatics & Biostatistics](https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/).
 
@@ -31,7 +19,7 @@ Be careful, RNAflow was mainly developped to run on the HPC of Institut Pasteur,
 <img src="images/rulegraph.svg" width="1000">
 
 
-## How to install RNAflow ?
+# How to install RNAflow ?
 
 
 You need to install:
@@ -58,9 +46,9 @@ In addition to above tools, you need to install pipeline-related tools:
 
 For Institut Pasteur HPC users, these tools are not required, they will be automatically loaded via module during pipeline running via the snakemake `--use-envmodules` instruction.
 
-## How to run RNAflow ?
+# How to run RNAflow ?
 
-### Usage
+## Usage
 
 * **Step 1: Install workflow**
 
@@ -132,7 +120,7 @@ run it in NNCR using environment modules via
 
 
 
-### Use case for human (or Eukaryotic) experiment
+## Use case for human (or Eukaryotic) experiment
 
 - Genome information
 
@@ -203,7 +191,7 @@ Why counting with Salmon and not STAR ? some informations here :
 
 
 
-### Use case for host-pathogen experiment
+## Use case for host-pathogen experiment
 
 - Genome information
 
@@ -278,7 +266,7 @@ Other tools are set to 'no'
 
 
 
-### Use case for bacteria (or prokaryotic) experiment
+## Use case for bacteria (or prokaryotic) experiment
 
 
 - Genome information
@@ -337,3 +325,23 @@ feature_counts:
 ```
 
 Other tools are set to 'no'
+
+
+
+
+## Authors
+
+* Rachel Legendre (@rlegendr)
+
+## Contributors
+
+* Adrien Pain
+* Claudia Chica
+* Elise Jacquemet
+* Emeline Perthame
+* Emmanuelle Permal
+* Hélène Lopez-Maestre
+* Hugo Varet
+* Natalia Pietrosemoli
+* Victoire Baillet
+* Vincent Guillemot
\ No newline at end of file