diff --git a/tools/graphlan/export2graphlan/export2graphlan.rules b/tools/graphlan/export2graphlan/SnakeFile
similarity index 100%
rename from tools/graphlan/export2graphlan/export2graphlan.rules
rename to tools/graphlan/export2graphlan/SnakeFile
diff --git a/tools/graphlan/graphlan/graphlan.rules b/tools/graphlan/graphlan/SnakeFile
similarity index 100%
rename from tools/graphlan/graphlan/graphlan.rules
rename to tools/graphlan/graphlan/SnakeFile
diff --git a/tools/graphlan/graphlan_annotate/graphlan_annotate.rules b/tools/graphlan/graphlan_annotate/SnakeFile
similarity index 100%
rename from tools/graphlan/graphlan_annotate/graphlan_annotate.rules
rename to tools/graphlan/graphlan_annotate/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2/metaphlan2.rules b/tools/metaphlan2/metaphlan2/SnakeFile
similarity index 100%
rename from tools/metaphlan2/metaphlan2/metaphlan2.rules
rename to tools/metaphlan2/metaphlan2/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2/usage_example.rules b/tools/metaphlan2/metaphlan2/usage_example.rules
index c60f1983a122c0f6b1e6bfab1ede6525280c3555..4b7e091e5c4c524568e2606f60638b62d8024bfd 100644
--- a/tools/metaphlan2/metaphlan2/usage_example.rules
+++ b/tools/metaphlan2/metaphlan2/usage_example.rules
@@ -19,7 +19,7 @@ __metaphlan2_input = "{dir}/{sample}.{ext}".format(dir=__input_dir,
                                                    ext=__metaphlan2_input_type + ".gz")
 __metaphlan2_output = "{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
                                                   sample="{sample}")
-include: "metaphlan2.rules"
+include: "SnakeFile"
 
 rule all:
     input:
diff --git a/tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules b/tools/metaphlan2/metaphlan2_heatmap/SnakeFile
similarity index 100%
rename from tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules
rename to tools/metaphlan2/metaphlan2_heatmap/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules b/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
index eb273eec8c7f2e3ec22b8d9310b3f7bd6f4e37aa..3d9acd0f231afb4b892f2071d8325dc7ca2a4aba 100644
--- a/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
+++ b/tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
@@ -17,7 +17,7 @@ __metaphlan2_heatmap_output_file_name = config['metaphlan2_heatmap'].get('output
 __metaphlan2_heatmap_input = __input
 __metaphlan2_heatmap_output = "{dir}/{file_name}".format(dir=__metaphlan2_heatmap_output_dir,
                                                          file_name=__metaphlan2_heatmap_output_file_name) 
-include: "metaphlan2_heatmap.rules"
+include: "SnakeFile"
 
 rule all:
     input:
diff --git a/tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules b/tools/metaphlan2/metaphlan2_merge/SnakeFile
similarity index 100%
rename from tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules
rename to tools/metaphlan2/metaphlan2_merge/SnakeFile
diff --git a/tools/metaphlan2/metaphlan2_merge/usage_example.rules b/tools/metaphlan2/metaphlan2_merge/usage_example.rules
index e1ba12a052e73985aa406f9f86bc5b69bd243df3..dd2f986117b1c85014d7f4290b32752a3f4e13e5 100644
--- a/tools/metaphlan2/metaphlan2_merge/usage_example.rules
+++ b/tools/metaphlan2/metaphlan2_merge/usage_example.rules
@@ -21,7 +21,7 @@ __metaphlan2_merge_input = expand("{dir}/{sample}.txt".format(dir=__input_dir,
                                   sample=config['samples'])
 __metaphlan2_merge_output = "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
                                                        file_name=__metaphlan2_merge_output_file_name) 
-include: "metaphlan2_merge.rules"
+include: "SnakeFile"
 
 rule all:
     input:
diff --git a/workflows/simple_metaphlan2/SnakeFile b/workflows/simple_metaphlan2/SnakeFile
index 37c6ca8a62de4c9854617e1484675a55158f7be2..5a7b2c0032f1209d789d451457c3d690378c2ebe 100644
--- a/workflows/simple_metaphlan2/SnakeFile
+++ b/workflows/simple_metaphlan2/SnakeFile
@@ -1,9 +1,9 @@
 configfile: "config.yaml"
 
 # ==== Rule paths ==== 
-__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")
+__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/SnakeFile")
+__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/SnakeFile")
+__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/SnakeFile")
 __graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/SnakeFile")
 
 __input_dir = config['input_dir']
diff --git a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
index d7ba7747434ce714a545d159e27cc2527e0c8eb9..0614069e23dd4ca14746bd06fa279a56f42d7536 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 = 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_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/SnakeFile")
+__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/SnakeFile")
+__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/SnakeFile")
 
 # ---- export2graphlan
 __export2graphlan_input = __graphlan_from_metaphlan2_input