flowcraft.generator.components.typing module¶
-
class
flowcraft.generator.components.typing.
SeqTyping
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Attributes: template_str
Class property that returns a populated template string
Methods
get_user_channel
(self, input_channel[, …])Returns the main raw channel for the process render
(template, context)Wrapper to the jinja2 render method from a template file set_channels
(self, \*\*kwargs)General purpose method that sets the main channels set_main_channel_names
(self, input_suffix, …)Sets the main channel names based on the provide input and output channel suffixes. set_param_id
(self, param_id)Sets the param_id for the process, which will be used to render the template. set_secondary_channel
(self, source, channel_list)General purpose method for setting a secondary channel update_attributes
(self, attr_dict)Updates the directives attribute from a dictionary object. update_main_forks
(self, sink)Updates the forks attribute with the sink channel destination update_main_input
-
class
flowcraft.generator.components.typing.
PathoTyping
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Attributes: template_str
Class property that returns a populated template string
Methods
get_user_channel
(self, input_channel[, …])Returns the main raw channel for the process render
(template, context)Wrapper to the jinja2 render method from a template file set_channels
(self, \*\*kwargs)General purpose method that sets the main channels set_main_channel_names
(self, input_suffix, …)Sets the main channel names based on the provide input and output channel suffixes. set_param_id
(self, param_id)Sets the param_id for the process, which will be used to render the template. set_secondary_channel
(self, source, channel_list)General purpose method for setting a secondary channel update_attributes
(self, attr_dict)Updates the directives attribute from a dictionary object. update_main_forks
(self, sink)Updates the forks attribute with the sink channel destination update_main_input
-
class
flowcraft.generator.components.typing.
Sistr
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Attributes: template_str
Class property that returns a populated template string
Methods
get_user_channel
(self, input_channel[, …])Returns the main raw channel for the process render
(template, context)Wrapper to the jinja2 render method from a template file set_channels
(self, \*\*kwargs)General purpose method that sets the main channels set_main_channel_names
(self, input_suffix, …)Sets the main channel names based on the provide input and output channel suffixes. set_param_id
(self, param_id)Sets the param_id for the process, which will be used to render the template. set_secondary_channel
(self, source, channel_list)General purpose method for setting a secondary channel update_attributes
(self, attr_dict)Updates the directives attribute from a dictionary object. update_main_forks
(self, sink)Updates the forks attribute with the sink channel destination update_main_input
-
class
flowcraft.generator.components.typing.
Momps
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Attributes: template_str
Class property that returns a populated template string
Methods
get_user_channel
(self, input_channel[, …])Returns the main raw channel for the process render
(template, context)Wrapper to the jinja2 render method from a template file set_channels
(self, \*\*kwargs)General purpose method that sets the main channels set_main_channel_names
(self, input_suffix, …)Sets the main channel names based on the provide input and output channel suffixes. set_param_id
(self, param_id)Sets the param_id for the process, which will be used to render the template. set_secondary_channel
(self, source, channel_list)General purpose method for setting a secondary channel update_attributes
(self, attr_dict)Updates the directives attribute from a dictionary object. update_main_forks
(self, sink)Updates the forks attribute with the sink channel destination update_main_input
-
class
flowcraft.generator.components.typing.
DengueTyping
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Attributes: template_str
Class property that returns a populated template string
Methods
get_user_channel
(self, input_channel[, …])Returns the main raw channel for the process render
(template, context)Wrapper to the jinja2 render method from a template file set_channels
(self, \*\*kwargs)General purpose method that sets the main channels set_main_channel_names
(self, input_suffix, …)Sets the main channel names based on the provide input and output channel suffixes. set_param_id
(self, param_id)Sets the param_id for the process, which will be used to render the template. set_secondary_channel
(self, source, channel_list)General purpose method for setting a secondary channel update_attributes
(self, attr_dict)Updates the directives attribute from a dictionary object. update_main_forks
(self, sink)Updates the forks attribute with the sink channel destination update_main_input
-
class
flowcraft.generator.components.typing.
Seroba
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Serotyping of Streptococcus pneumoniae sequencing data
Attributes: template_str
Class property that returns a populated template string
Methods
get_user_channel
(self, input_channel[, …])Returns the main raw channel for the process render
(template, context)Wrapper to the jinja2 render method from a template file set_channels
(self, \*\*kwargs)General purpose method that sets the main channels set_main_channel_names
(self, input_suffix, …)Sets the main channel names based on the provide input and output channel suffixes. set_param_id
(self, param_id)Sets the param_id for the process, which will be used to render the template. set_secondary_channel
(self, source, channel_list)General purpose method for setting a secondary channel update_attributes
(self, attr_dict)Updates the directives attribute from a dictionary object. update_main_forks
(self, sink)Updates the forks attribute with the sink channel destination update_main_input