Update snakefile generation tools

generate_tool_snakefile.py

@@ -43,21 +43,21 @@ def generate(name):
 
                 size_inputs = len(cmd_inputs)
 
-                if(size_inputs == 0):
-                    result += "\t\t**" + name + "_inputs(),\n"
+                #if(size_inputs == 0):
+                result += "\t\t**" + name + "_inputs(),\n"
 
                 for input in cmd_inputs:
 
                     if "name" in input: 
 
-                        if input['name'] == "reads":
-                            result += "\t\t**" + name + "_inputs(),\n"
+                        # if input['name'] == "reads":
+                        #     result += "\t\t**" + name + "_inputs(),\n"
 
-                        elif "directory" in input:
+                        if "directory" in input:
 
                             result += "\t\t" +  input['name'] + " = " + result_dir + " + \"/\"" + " + \"" + input['directory'] + "\",\n" 
 
-                        elif "file" in input:
+                        if "file" in input:
 
                             result += "\t\t" +  input['name'] + " = " + result_dir + " + \"/\"" + " + \"" + input['file'] + "\",\n" 
 

generate_workflow_snakefile.py

@@ -146,14 +146,14 @@ def generate(name):
 
     result += "{import global_rules}\n"
 
-    print(result)
+    #print(result)
 
     
 
-    #path_snakefile = PATH_INPUT + "/" + name + "/" + name + ".snakefile"
-    #f = open(path_snakefile, "w")
-    #f.write(result)
-    #f.close()
+    path_snakefile = PATH_INPUT + "/" + name + "/" + name + ".snakefile"
+    f = open(path_snakefile, "w")
+    f.write(result)
+    f.close()