diff --git a/workflows/simple_metaphlan2/SnakeFile b/workflows/simple_metaphlan2/SnakeFile
index 8f939955b32bcf28fbd533248bcc31fe72b3f717..37c6ca8a62de4c9854617e1484675a55158f7be2 100644
--- a/workflows/simple_metaphlan2/SnakeFile
+++ b/workflows/simple_metaphlan2/SnakeFile
@@ -1,10 +1,10 @@
 configfile: "config.yaml"
 
 # ==== Rule paths ==== 
-__metaphlan2_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
-__metaphlan2_merge_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
-__metaphlan2_heatmap_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
-__graphlan_from_metaphlan2_rules = "../subworkflows/graphlan_from_metaphlan2/SnakeFile"
+__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/metaphlan2.rules")
+__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules")
+__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules")
+__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/SnakeFile")
 
 __input_dir = config['input_dir']
 __main_output_dir = config.get('output_dir', 'output')
diff --git a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
index dfd7278541c6e45454f5bb3cfa487759d7428d09..d7ba7747434ce714a545d159e27cc2527e0c8eb9 100644
--- a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
+++ b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
@@ -8,9 +8,9 @@ This subworkflow need to be called to be used by specifying:
 """
 
 # ==== Rule paths ==== 
-__export2graphlan_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
-__graphlan_annotate_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
-__graphlan_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
+__export2graphlan_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/metaphlan2.rules")
+__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules")
+__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules")
 
 # ---- export2graphlan
 __export2graphlan_input = __graphlan_from_metaphlan2_input