flowcraft.generator.components.assembly module

class flowcraft.generator.components.assembly.Bcalm(**kwargs)

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)

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)

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)

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)

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)

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