flowcraft.generator.components.assembly_processing module¶
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class
flowcraft.generator.components.assembly_processing.
ProcessSkesa
(**kwargs)[source]¶ Bases:
flowcraft.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_param_id
(param_id)Sets the param_id for the process, which will be used to render the template. 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
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class
flowcraft.generator.components.assembly_processing.
ProcessSpades
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Process spades process template interface
This process is set with:
input_type
: assemblyoutput_type
: assemblyptype
: 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_param_id
(param_id)Sets the param_id for the process, which will be used to render the template. 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
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class
flowcraft.generator.components.assembly_processing.
AssemblyMapping
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Assembly mapping process template interface
This process is set with:
input_type
: assemblyoutput_type
: assemblyptype
: 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 processSTATUS_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_param_id
(param_id)Sets the param_id for the process, which will be used to render the template. 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
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class
flowcraft.generator.components.assembly_processing.
Pilon
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Pilon mapping process template interface
This process is set with:
input_type
: assemblyoutput_type
: assemblyptype
: 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_param_id
(param_id)Sets the param_id for the process, which will be used to render the template. 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
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class
flowcraft.generator.components.assembly_processing.
Bandage
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Visualize the assembly using Bandage
This process is set with:
input_type
: assemblyoutput_type
: noneptype
: 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_param_id
(param_id)Sets the param_id for the process, which will be used to render the template. 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
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class
flowcraft.generator.components.assembly_processing.
Quast
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Assess assembly quality using QUAST
This process is set with:
input_type
: assemblyoutput_type
: tsvptype
: 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_param_id
(param_id)Sets the param_id for the process, which will be used to render the template. 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