diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py index ae780ae65ce6e658edf9d38e5eecdf3857cfb119..0c44921721a72a713ab16c94682d23ac71d2a8ee 100644 --- a/src/nextflow_building_blocks.py +++ b/src/nextflow_building_blocks.py @@ -80,6 +80,9 @@ class Nextflow_Building_Blocks: def get_name_file(self): return self.origin.get_name_file() + def get_root_directory(self): + return self.origin.get_root_directory() + def get_rocrate_key(self, dico): return f"{self.get_file_address()[len(dico['temp_directory'])+1:]}#{self.get_name()}" diff --git a/src/nextflow_file.py b/src/nextflow_file.py index bc296df628a9d40ade5628d1256b14a18946d401..9299da5c0947f3d1eacc4f81e03472cf866d113e 100644 --- a/src/nextflow_file.py +++ b/src/nextflow_file.py @@ -208,11 +208,7 @@ class Nextflow_File(Nextflow_Building_Blocks): def get_file_address(self): return os.path.normpath(self.file) - def get_root_directory(self): - if(self.origin==None): - return '/'.join(self.get_file_address().split('/')[:-1]) - else: - return self.origin.get_root_directory() + #Returns either a subworkflow or process from the name def get_element_from_name(self, name): diff --git a/src/outils_graph.py b/src/outils_graph.py index f1da30a29d0acc2fd6faefed382de8f0c1156b7d..b754f91b62913a41604efe9886c43273b99a8e3e 100644 --- a/src/outils_graph.py +++ b/src/outils_graph.py @@ -146,8 +146,8 @@ def generate_graph_dot(filename, dico, label_node = True, label_edge = True, ren fill_dot(dot, dico, label_node, label_edge) #metro_dot(dot, dico, relevant_nodes = relevant_nodes) dot.save(filename=f'{filename}.dot') - dot.format = 'dot' - dot.render(filename=f'{filename}_pos') + #dot.format = 'dot' + #dot.render(filename=f'{filename}_pos') if(render_graphs): dot.render(filename=f'{filename}.dot', outfile=f'{filename}.png') diff --git a/src/process.py b/src/process.py index d593bd5189882f626764e221a993f77b2eac21f5..464852351c13675f117a60f5ac6e1cd4f5b40203 100644 --- a/src/process.py +++ b/src/process.py @@ -461,7 +461,8 @@ class Process(Nextflow_Building_Blocks): self.initialise_name() self.initialise_parts() self.initialise_inputs_outputs() - annotations = self.get_processes_annotation() + #annotations = self.get_processes_annotation() + annotations = None if(annotations!=None): self.tools = annotations[self.get_code()]["tools"] self.commands = annotations[self.get_code()]["commands"] diff --git a/src/workflow.py b/src/workflow.py index d2ab751c74d35bd1e51558b7b5204e788975b72a..9252627ab47b644798d193394d7f703dc8824530 100644 --- a/src/workflow.py +++ b/src/workflow.py @@ -146,6 +146,9 @@ class Workflow: """ return self.address + def get_root_directory(self): + return '/'.join(self.get_address().split('/')[:-1]) + def get_workflow_directory(self): """Method that returns the workflow directory