assemblerflow.generator.components.assembly_processing module

class assemblerflow.generator.components.assembly_processing.ProcessSkesa(**kwargs)[source]

Bases: assemblerflow.generator.process.Process

Attributes:
template_str

Class property that returns a populated template string

Methods

get_user_channel(input_channel[, input_type]) Returns the main raw channel for the process
render(template, context) Wrapper to the jinja2 render method from a template file
set_channels(**kwargs) General purpose method that sets the main channels
set_main_channel_names(input_suffix, …) Sets the main channel names based on the provide input and output channel suffixes.
set_secondary_channel(source, channel_list) General purpose method for setting a secondary channel
update_attributes(attr_dict) Updates the directives attribute from a dictionary object.
update_main_forks(sink) Updates the forks attribute with the sink channel destination
update_main_input  
class assemblerflow.generator.components.assembly_processing.ProcessSpades(**kwargs)[source]

Bases: assemblerflow.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(input_channel[, input_type]) Returns the main raw channel for the process
render(template, context) Wrapper to the jinja2 render method from a template file
set_channels(**kwargs) General purpose method that sets the main channels
set_main_channel_names(input_suffix, …) Sets the main channel names based on the provide input and output channel suffixes.
set_secondary_channel(source, channel_list) General purpose method for setting a secondary channel
update_attributes(attr_dict) Updates the directives attribute from a dictionary object.
update_main_forks(sink) Updates the forks attribute with the sink channel destination
update_main_input  
class assemblerflow.generator.components.assembly_processing.AssemblyMapping(**kwargs)[source]

Bases: assemblerflow.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(input_channel[, input_type]) Returns the main raw channel for the process
render(template, context) Wrapper to the jinja2 render method from a template file
set_channels(**kwargs) General purpose method that sets the main channels
set_main_channel_names(input_suffix, …) Sets the main channel names based on the provide input and output channel suffixes.
set_secondary_channel(source, channel_list) General purpose method for setting a secondary channel
update_attributes(attr_dict) Updates the directives attribute from a dictionary object.
update_main_forks(sink) Updates the forks attribute with the sink channel destination
update_main_input  
class assemblerflow.generator.components.assembly_processing.Pilon(**kwargs)[source]

Bases: assemblerflow.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(input_channel[, input_type]) Returns the main raw channel for the process
render(template, context) Wrapper to the jinja2 render method from a template file
set_channels(**kwargs) General purpose method that sets the main channels
set_main_channel_names(input_suffix, …) Sets the main channel names based on the provide input and output channel suffixes.
set_secondary_channel(source, channel_list) General purpose method for setting a secondary channel
update_attributes(attr_dict) Updates the directives attribute from a dictionary object.
update_main_forks(sink) Updates the forks attribute with the sink channel destination
update_main_input