flowcraft.generator.components.annotation module

class flowcraft.generator.components.annotation.Abricate(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Abricate mapping process template interface

This process is set with:

  • input_type: assembly
  • output_type: None
  • ptype: post_assembly

It contains one secondary channel link end:

  • MAIN_assembly (alias: MAIN_assembly): Receives the last

assembly.

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.annotation.CardRgi(**kwargs)[source]

Bases: flowcraft.generator.process.Process

card’s rgi process template interface

This process is set with:

  • input_type: fasta
  • output_type: txt
  • ptype: resistance gene detection (assembly)
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.annotation.Prokka(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Prokka mapping process template interface

This process is set with:

  • input_type: assembly
  • output_type: None
  • ptype: post_assembly

It contains one secondary channel link end:

  • MAIN_assembly (alias: MAIN_assembly): Receives the last

assembly.

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.annotation.Diamond(**kwargs)[source]

Bases: flowcraft.generator.process.Process

diamond process for protein database queries

This process is set with:

  • input_type: fasta
  • output_type: None
  • ptype: post_assembly
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