From efef592d6959f2f1f32704f1c3508a99220a5539 Mon Sep 17 00:00:00 2001
From: Midoux Cedric <cedric.midoux@irstea.fr>
Date: Mon, 22 Jun 2020 18:38:21 +0200
Subject: [PATCH] First update README.md

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 README.md | 45 ++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 44 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
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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.
-- 
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