From 744b3b0d358213320ec78574e3bdcb83da4c0e49 Mon Sep 17 00:00:00 2001
From: antux18 <antux18@gmail.com>
Date: Thu, 15 Aug 2024 12:32:39 +0200
Subject: [PATCH] Added doc for running the Snakemake workflow.

---
 README.md | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 2ee5232..4c8ed2c 100644
--- a/README.md
+++ b/README.md
@@ -58,7 +58,14 @@ Otherwise, you can use the Nix package manager and run `nix develop` in this dir
 
 ### Running the whole workflow
 
-*TODO: write the doc*
+First, open `config/config.yaml` and change `system` to `local` if you try to run the workflow outside of the Grid'5000 testbed.
+
+Then, run the following command at the root directory of the repository:
+```
+snakemake --cores <nb_cores>
+```
+
+Where `<nb_cores>` is the number of cores you want to assign to the workflow. The number of cores determine the number of instances of ECG that can run in parallel, so you may want to assign as many cores as possible here.
 
 ### Running each component separately
 
@@ -145,7 +152,7 @@ Where:
 - `<input_table1>`, `<input_table2>`... are one or more output tables from ECG. The required ECG output depends on the analysis script, see below.
 - `<output_table>` is the path where to store the table generated by the analysis script.
 
-*TODO: explain outputs*
+*TODO: explain the content of the output files*
 
 ##### Software environment analysis