fix Snakefile names

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: "SnakeFile"
+include: "Snakefile"
 
 rule all:
     input:

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: "SnakeFile"
+include: "Snakefile"
 
 rule all:
     input:

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: "SnakeFile"
+include: "Snakefile"
 
 rule all:
     input:

workflows/simple_metaphlan2/SnakeFile → workflows/simple_metaphlan2/Snakefile

 configfile: "config.yaml"
 
 # ==== Rule paths ==== 
-__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")
+__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']
 __main_output_dir = config.get('output_dir', 'output')
@@ -39,7 +39,7 @@ include: __metaphlan2_heatmap_rules
 
 # ---- Graphlan Dendogram
 __graphlan_from_metaphlan2_output_dir = __main_output_dir + "/graphlan"
-__graphlan_from_metaphlan2_output_file_name = config['graphlan_from_metaphlan2'].get('output_name',"dendogram.png")
+__graphlan_from_metaphlan2_output_file_name =  config.get("graphlan_from_metaphlan2", {}).get('output_name',"dendogram.png")
 __graphlan_from_metaphlan2_input = __metaphlan2_merge_output
 __graphlan_from_metaphlan2_output = "{dir}/{file_name}".format(dir=__graphlan_from_metaphlan2_output_dir,
                                                          file_name=__graphlan_from_metaphlan2_output_file_name) 

workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile → workflows/subworkflows/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/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_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