diff --git a/biobb_common/generic/biobb_object.py b/biobb_common/generic/biobb_object.py index 2816472..3791955 100644 --- a/biobb_common/generic/biobb_object.py +++ b/biobb_common/generic/biobb_object.py @@ -22,14 +22,8 @@ class BiobbObject: Args: properties (dict - Python dictionary object containing the tool parameters, not input/output files): - * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. - * **disable_sandbox** (*bool*) - (False) Disable the use of temporal unique directories aka sandbox. Only for local execution. - * **chdir_sandbox** (*bool*) - (False) Change directory to the sandbox using just file names in the command line. Only for local execution. - * **dev** (*str*) - (None) Adding additional options to command line. - * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. - * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. - * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. - * **env_vars_dict** (*dict*) - ({}) Environment Variables Dictionary. + + * **io_dict** (*dict*) - ({}) Input/Output files dictionary. * **container_path** (*str*) - (None) Path to the binary executable of your container. * **container_image** (*str*) - (None) Container Image identifier. * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container. @@ -37,6 +31,35 @@ class BiobbObject: * **container_user_id** (*str*) - (None) User number id to be mapped inside the container. * **container_shell_path** (*str*) - ("/bin/bash -c") Path to the binary executable of the container shell. * **container_generic_command** (*str*) - ("run") Which command typically run or exec will be used to execute your image. + * **stage_io_dict** (*dict*) - ({}) Stage Input/Output files dictionary. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. + * **disable_sandbox** (*bool*) - (False) Disable the use of temporal unique directories aka sandbox. Only for local execution. + * **global_properties_list** (*list*) - ([]) List of global properties. + * **chdir_sandbox** (*bool*) - (False) Change directory to the sandbox using just file names in the command line. Only for local execution. + * **binary_path** (*str*) - ('') Path to the binary executable. + * **can_write_console_log** (*bool*) - (True) Can write console log. + * **global_log** (*Logger object*) - (None) Log from the main workflow. + * **out_log** (*Logger object*) - (None) Log from the step. + * **err_log** (*Logger object*) - (None) Error log from the step. + * **prefix** (*str*) - (None) Prefix if provided. + * **step** (*str*) - (None) Name of the step. + * **path** (*str*) - ('') Absolute path to the step working dir. + * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. + * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **cmd** (*list*) - ([]) Command line list, NOT read from the dictionary. + * **return_code** (*int*) - (0) Return code of the command execution, NOT read from the dictionary. + * **timeout** (*int*) - (None) Timeout for the execution of the command. + * **tmp_files** (*list*) - ([]) List of temporal files, NOT read from the dictionary. + * **env_vars_dict** (*dict*) - ({}) Environment Variables Dictionary. + * **shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the shell. + * **dev** (*str*) - (None) Development options. + * **check_extensions** (*bool*) - (True) Check extensions of the input/output files. + * **check_var_typing** (*bool*) - (True) Check typing of the input/output files. + * **locals_var_dict** (*dict*) - ({}) Local variables dictionary. + * **doc_arguments_dict** (*dict*) - ({}) Documentation arguments dictionary. + * **doc_properties_dict** (*dict*) - ({}) Documentation properties dictionary. + + """ def __init__(self, properties=None, **kwargs) -> None: # type: ignore