add possibility to change ref path to rules in config files

workflows/simple_metaphlan2/SnakeFile

 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')

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