flowcraft.generator.components.assembly_processing module

class flowcraft.generator.components.assembly_processing.ProcessSkesa(**kwargs)

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.assembly_processing.ProcessSpades(**kwargs)

Bases: flowcraft.generator.process.Process

Process spades process template interface

This process is set with:

• input_type: assembly
• output_type: assembly
• 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

class flowcraft.generator.components.assembly_processing.AssemblyMapping(**kwargs)

Bases: flowcraft.generator.process.Process

Assembly mapping process template interface

This process is set with:

• input_type: assembly
• output_type: assembly
• ptype: post_assembly

It contains one secondary channel link end:

• MAIN_fq (alias: _MAIN_assembly): Receives the FastQ files

from the last process with fastq output type.

It contains two status channels:

• STATUS_am: Status for the assembly_mapping process
• STATUS_amp: Status for the process_assembly_mapping 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.assembly_processing.Pilon(**kwargs)

Bases: flowcraft.generator.process.Process

Pilon mapping process template interface

This process is set with:

• input_type: assembly
• output_type: assembly
• ptype: post_assembly

It contains one dependency process:

• assembly_mapping: Requires the BAM file generated by the

assembly mapping 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.assembly_processing.Bandage(**kwargs)

Bases: flowcraft.generator.process.Process

Visualize the assembly using Bandage

This process is set with:

• input_type: assembly
• 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

class flowcraft.generator.components.assembly_processing.Quast(**kwargs)

Bases: flowcraft.generator.process.Process

Assess assembly quality using QUAST

This process is set with:

• input_type: assembly
• output_type: tsv
• 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