added some methods to thr process class

src/process.py

@@ -19,6 +19,7 @@ class Process(Nextflow_Building_Blocks):
         self.input_code = ""
         self.output_code = ""
         self.when_code = ""
+        self.pusblishDir_code = ""
         self.script_code = ""
         self.tools = []
         self.modules = []
@@ -103,7 +104,7 @@ class Process(Nextflow_Building_Blocks):
         packages = []
         packages+= self.get_python_packages_imported_internal_script()
         packages+= self.get_python_packages_imported_external_scripts()
-        return packages
+        return list(set(packages))
 
 
     def get_R_libraries_loaded_internal_script(self):
@@ -122,7 +123,7 @@ class Process(Nextflow_Building_Blocks):
         libraries = []
         libraries+= self.get_R_libraries_loaded_internal_script()
         libraries+= self.get_R_libraries_loaded_external_scripts()
-        return libraries
+        return list(set(libraries))
             
     #TODO -> do the same with Ruby/PErl scripts
 
@@ -155,6 +156,11 @@ class Process(Nextflow_Building_Blocks):
 
     
     
+    def get_input_code_lines(self):
+        tab = []
+        for l in self.input_code.split('\n'):
+            tab.append(l.strip())
+        return tab
 
     def get_inputs(self):
         return self.inputs
@@ -165,6 +171,12 @@ class Process(Nextflow_Building_Blocks):
     def get_outputs(self):
         return self.outputs
     
+    def get_output_code_lines(self):
+        tab = []
+        for l in self.output_code.split('\n'):
+            tab.append(l.strip())
+        return tab
+    
     def get_nb_outputs(self):
         return len(self.outputs)
     
@@ -184,6 +196,14 @@ class Process(Nextflow_Building_Blocks):
         temp_code = temp_code[:-1].strip()
         if(len(temp_code)==0):
             raise BioFlowInsightError(f"The process '{self.get_name()}' defined in the file '{self.get_file_address()}' is an empty process!", num = 22, origin=self)
+    
+        publishDir_multiple, publishDir_pos= False, (0, 0)
+        for match in re.finditer(r"publishDir", code):
+            #if(publishDir_multiple):
+            #    raise BioFlowInsightError(f"Multiple 'publishDir' were found in the process '{self.get_name()}'.", num = 22, origin=self)
+            publishDir_pos = match.span(0)
+            publishDir_multiple = True
+
         input_multiple, input_pos= False, (0, 0)
         for match in re.finditer(constant.INPUT, code):
             if(input_multiple):
@@ -210,8 +230,8 @@ class Process(Nextflow_Building_Blocks):
             script_pos = match.span(0)
             break
 
-        positions = [input_pos, output_pos, when_pos, script_pos]
-        variables_index = ['input', 'output', 'when', 'script']
+        positions = [publishDir_pos, input_pos, output_pos, when_pos, script_pos]
+        variables_index = ['pusblishDir', 'input', 'output', 'when', 'script']
         positions, variables_index = sort_and_filter(positions, variables_index)
         
 
@@ -226,6 +246,8 @@ class Process(Nextflow_Building_Blocks):
                 self.input_code = temp_code
             elif(variables_index[i]=='output'):
                 self.output_code = temp_code
+            elif(variables_index[i]=='pusblishDir'):
+                self.pusblishDir_code = temp_code
             elif(variables_index[i]=='when'):
                 self.when_code = temp_code
             elif(variables_index[i]=='script'):
@@ -305,11 +327,20 @@ class Process(Nextflow_Building_Blocks):
     
     def get_input_parameters(self):
         code = self.get_input_code()
+
+        #This is to remove the from for the DSL1 processes
+        #But also remoce the 'stageAs'
+        lines = code.split('\n')
+        code = ""
+        for l in lines:
+            code+=l.split(" from ")[0].split("stageAs")[0]
+            code+'\n'
+
         parameters = []
-        for match in re.finditer(r"\w+", code):
+        for match in re.finditer(r"\w+(\.\w+)*", code):
             parameters.append(match.group(0))
         parameters = list(set(parameters))#Here we can a unique cause a parameter can only be given once in any case
-        words_2_remove = ["path", "val", "tuple", "into", "stageAs", "emit"]
+        words_2_remove = ["path", "val", "tuple", "into", "stageAs", "emit", "file", "set"]
         for word in words_2_remove:
             try:
                 parameters.remove(word)