Update generators scripts to fit step_name param

generate_sag_yaml.py

@@ -58,7 +58,7 @@ def get_params_to_remove(pipeline):
                 to_remove.append(line["param_B"])
     return to_remove
 
-def generate_tool(toolname, pipeline):
+def generate_tool(toolname, pipeline, step_name):
     to_remove = get_params_to_remove(pipeline)
     template = yaml.load(tool_template, Loader=yaml.FullLoader)
     tool = read_yaml("tools/" + toolname + "/" + toolname + ".yaml")
@@ -70,6 +70,7 @@ def generate_tool(toolname, pipeline):
         for option in command["options"]:
             if option not in template["content"]:
                 if option["name"] not in to_remove:
+                    option["name"] = step_name + "__" + option["name"]
                     template["content"].append(option)
 
     template["content"].append(
@@ -180,7 +181,7 @@ def generate_sag_yaml(pipeline, template, outdir):
         # for each tool in a step, create a box
         for tool in step["tools"]:
             # predefined boxes
-            template["App"]["pages"][page_number]["boxes"].append(generate_tool(tool,pipeline))
+            template["App"]["pages"][page_number]["boxes"].append(generate_tool(tool,pipeline,step["name"]))
         page_number += 1
 
     return template

generate_tool_snakefile.py

@@ -29,9 +29,9 @@ def generate(name):
 
         for cmd in yaml['commands']:
 
-            result += "rule " + cmd['name'] + ":\n"
+            result += "rule <step_name>__" + cmd['name'] + ":\n"
 
-            rule_dir = "config[\"" + cmd['name'] + "_output_dir\"]"
+            rule_dir = "config[\"<step_name>__" + cmd['name'] + "_output_dir\"]"
 
             # input 
 
@@ -44,7 +44,7 @@ def generate(name):
                 size_inputs = len(cmd_inputs)
 
                 #if(size_inputs == 0):
-                result += "\t\t**" + name + "_inputs(),\n"
+                result += "\t\t**<step_name>__" + name + "_inputs(),\n"
 
                 for input in cmd_inputs:
 
@@ -75,7 +75,7 @@ def generate(name):
                             if option['type'] == "input_file":
 
                                 if "name" in option:
-                                    result += "\t\t" + option['name'].replace(cmd["name"]+"_","").replace(name+"_","") + " = " + "config[\"" + option['name'] + "\"],\n"
+                                    result += "\t\t" + option['name'].replace(cmd["name"]+"_","").replace(name+"_","") + " = " + "config[\"<step_name>__" + option['name'] + "\"],\n"
                                     #result += "\t\tinput_file_p" + str(count_input) + " = " + "config[\"" + option['name'] + "\"],\n"
                                     count_input += 1
 
@@ -116,6 +116,9 @@ def generate(name):
 
             result += "\t\toutput_dir = " + result_dir + " + \"/\" + " + rule_dir + "+ \"/" + sample_output + "\",\n"
 
+            if "command" in cmd:
+                result += "\t\tcommand = config[\"<step_name>__" + cmd['name'] + "_command\"],\n"
+
             if "options" in cmd:
                 
                 cmd_options = cmd['options']
@@ -128,8 +131,7 @@ def generate(name):
 
                             if "_threads" not in option['name']:
 
-                                result += "\t\t" + option['name'].replace(cmd["name"]+"_","").replace(name+"_","") + " = " + "config[\""+option['name']+"\"],\n"
-          
+                                result += "\t\t" + option['name'].replace(cmd["name"]+"_","").replace(name+"_","") + " = " + "config[\"<step_name>__"+option['name']+"\"],\n"
 
             # log 
 
@@ -137,7 +139,7 @@ def generate(name):
 
                 result += "\n\tlog: \n"
 
-                result += "\t\t" + result_dir + " + \"/logs/" + cmd['name'] + "/" + sample + cmd['name'] + "_log.txt\"\n"
+                result += "\t\t" + result_dir + " + \"/logs/\" + " + rule_dir + " + \"/" + sample + cmd['name'] + "_log.txt\"\n"
 
             # threads
 
@@ -150,7 +152,7 @@ def generate(name):
                 if "name" in option: 
 
                     if "_threads" in option['name']:
-                        result += "\n\t\tconfig[\"" + option['name'] + "\"]\n"
+                        result += "\n\t\tconfig[\"<step_name>__" + option['name'] + "\"]\n"
                         count_thread += 1
 
             if count_thread == 0:
@@ -167,7 +169,7 @@ def generate(name):
 
                 #for shell in cmd_shell:
                 #    result += "\t\t\"" + shell + "\"\n"
-                result += "\t\t\"" + cmd_shell + "\"\n"
+                result += "\t\t\"{params.command}\"\n"
             
 
             # End cmd
@@ -176,7 +178,7 @@ def generate(name):
 
         # End loop cmd
 
-    # print(result)
+    #print(result)
 
     path_snakefile = PATH_INPUT + "/" + name + "/" + name + ".rule.snakefile"
     f = open(path_snakefile, "w")

generate_workflow_snakefile.py

@@ -70,15 +70,15 @@ def generate(name):
 
             if "rule_name" in step:
 
-                result += "def " + step["rule_name"] + "_inputs():\n"
+                result += "def " + step["step_name"] + "__" + step["rule_name"] + "_inputs():\n"
                 result += "\tinputs = dict()\n"
 
                 if "params" in step:
                     for param in step["params"]:
                         if "raw_" in param["origin_command"] :
-                            result += "\tinputs[\"" + param["input_name"] + "\"] = "+param["origin_command"]+"[\""+param["origin_name"]+"\"]\n"
+                            result += "\tinputs[\"" + param["input_name"] + "\"] = " + param["origin_command"]+"[\""+param["origin_name"]+"\"]\n"
                         else:
-                            result += "\tinputs[\"" + param["input_name"] + "\"] = rules." + param["origin_command"] + ".output." + param["origin_name"] + "\n"
+                            result += "\tinputs[\"" + param["input_name"] + "\"] = rules." + param["origin_step"] + "__" + param["origin_command"] + ".output." + param["origin_name"] + "\n"
 
                 result += "\treturn inputs\n"
                 result += "\n"
@@ -111,7 +111,7 @@ def generate(name):
                 if ("_PE" in step["rule_name"]):
                     add = "and config['SeOrPe'] == 'PE'"
                 result += "\tif (step == \"" + step["step_name"] + "\" " + add + " ):\n"
-                result += "\t\toutputs = rules." + step["rule_name"] + ".output\n"
+                result += "\t\toutputs = rules." + step["step_name"] + "__" + step["rule_name"] + ".output\n"
                 result += "\t\t\n"