diff --git a/.gitmodules b/.gitmodules
index 7c71e27..e2aec42 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "mnutils"]
-	path = mnutils
+	path = workflow/mnutils
 	url = git@github.com:Swart-lab/mnutils.git
diff --git a/Snakefile b/workflow/Snakefile
similarity index 100%
rename from Snakefile
rename to workflow/Snakefile
diff --git a/adapters.fasta b/workflow/adapters.fasta
similarity index 100%
rename from adapters.fasta
rename to workflow/adapters.fasta
diff --git a/cluster.json b/workflow/cluster.json
similarity index 100%
rename from cluster.json
rename to workflow/cluster.json
diff --git a/config.yaml b/workflow/config.yaml
similarity index 100%
rename from config.yaml
rename to workflow/config.yaml
diff --git a/envs/mappers.yml b/workflow/envs/mappers.yml
similarity index 100%
rename from envs/mappers.yml
rename to workflow/envs/mappers.yml
diff --git a/envs/mnutils.yml b/workflow/envs/mnutils.yml
similarity index 100%
rename from envs/mnutils.yml
rename to workflow/envs/mnutils.yml
diff --git a/mnutils b/workflow/mnutils
similarity index 100%
rename from mnutils
rename to workflow/mnutils