From 6e5ea35fb4df28d5f3236cbbf8a9aaf904866a4f Mon Sep 17 00:00:00 2001
From: alvaannett <46521652+alvaannett@users.noreply.github.com>
Date: Wed, 6 Sep 2023 13:14:16 -0400
Subject: [PATCH] Update README.md

---
 README.md | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e925afb..9066f90 100644
--- a/README.md
+++ b/README.md
@@ -241,7 +241,27 @@ snakemake -s ${snakefile} --configfile ${config} ${extra_config} --cores 5
 
 #  Outputs 
 
-ADD DESCRIPTION OF OUTPUTS 
+## Output folder structure 
+
+In each output folder there will be one folder per sample as well as a folder for the models. In each sample folder and in the model folder there will be subfolders for each reference specified in the config file. Each sample folder will also contain a reports folder with a `.html` report with the prediction results. Each refrence folder contains sub folders for the individual tools model and prediction results. 
+
+```
+out/
+├── sample1
+│   ├── reference1
+│   ├── reference2
+│   └── report
+├── sample1
+│   ├── reference1
+│   ├── reference2
+│   └── report
+└── model
+    ├── reference1
+    └── reference2
+```
+
+## Output files 
+
 
 # :gear: Installation and Dependencies