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-# workflow_metagenomics
+# Workflow Metagenomics
 
+This pipeline is currently adapted for use on the [INRAE MIGALE](https://migale.inrae.fr/) cluster.
+
+## Settings
+
+In this folder, in a parent folder `../my_project` :
+
+* Place the raw data in the folder `DATA/raw/` (or `../my_project/DATA/raw/`).
+* Edit the file [`config.json`](config.json)
+* Adapt the file [`cluster.json`](cluster.json)
+* Select the desired outputs in the file [`global.smk`](global.smk)
+
+## Running
+
+For simple use :
+
+```bash
+./RunSnake.sh global.smk
+```
+
+For a dry-run :
+
+```bash
+./RunSnake_printshellcmds.sh global.smk
+```
+
+For a SGE submission :
+
+```bash
+./qsubSnake.sh global.smk
+```
+
+For a jobs visualisation :
+
+```bash
+./RunSnake_graph.sh global.smk
+```
+
+## Results
+
+All results are available :
+
+* In the folder `work/` for intermediate results,
+* In the folder `report/` for reports.