flowcraft.generator.components.assembly module¶
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class
flowcraft.generator.components.assembly.
Bcalm
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Bcalm process template interface
This process is set with:
input_type
: fastqoutput_type
: assemblyptype
: 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.
Spades
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Spades process template interface
This process is set with:
input_type
: fastqoutput_type
: assemblyptype
: 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
(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.
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
(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.
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
(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.
Abyss
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
ABySS process template interface
This process is set with:
input_type
: fastqoutput_type
: assemblyptype
: 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.
Unicycler
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Unicycler process template interface
This process is set with:
input_type
: fastqoutput_type
: assemblyptype
: 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