flowcraft.generator.components.assembly module

class flowcraft.generator.components.assembly.Bcalm(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Bcalm process template interface

This process is set with:

  • input_type: fastq
  • output_type: assembly
  • ptype: 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.assembly.Spades(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Spades process template interface

This process is set with:

  • input_type: fastq
  • output_type: assembly
  • ptype: assembly

It contains one secondary channel link end:

  • SIDE_max_len (alias: SIDE_max_len): Receives max read length
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.assembly.Skesa(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Skesa process template interface

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.assembly.ViralAssembly(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Process to assemble viral genomes, based on SPAdes and megahit

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.assembly.Abyss(**kwargs)[source]

Bases: flowcraft.generator.process.Process

ABySS process template interface

This process is set with:

  • input_type: fastq
  • output_type: assembly
  • ptype: 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.assembly.Unicycler(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Unicycler process template interface

This process is set with:

  • input_type: fastq
  • output_type: assembly
  • ptype: 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