flowcraft.generator.components.metagenomics module¶

class flowcraft.generator.components.metagenomics.Kraken(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

kraken process template interface

This process is set with:

input_type: fastq

output_type: txt

ptype: taxonomic classification

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

class flowcraft.generator.components.metagenomics.Kraken2(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

kraken2 process template interface

This process is set with:

input_type: fastq

output_type: txt

ptype: taxonomic classification

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

class flowcraft.generator.components.metagenomics.Maxbin2(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

MaxBin2, a metagenomics binning software

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.

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

class flowcraft.generator.components.metagenomics.Megahit(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

megahit 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`(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

class flowcraft.generator.components.metagenomics.Metaspades(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

Metaspades 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`(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

class flowcraft.generator.components.metagenomics.Midas_species(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

Midas species process template interface

This process is set with:

input_type: fastq

output_type: txt

ptype: taxonomic classification (species)

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

class flowcraft.generator.components.metagenomics.RemoveHost(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

bowtie2 to remove host reads process template interface

This process is set with:

input_type: fastq

output_type: fastq

ptype: removal os host reads

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

class flowcraft.generator.components.metagenomics.Metaprob(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

MetaProb to bin metagenomic reads interface

This process is set with:

input_type: fastq

output_type: csv

ptype: binning of reads

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

class flowcraft.generator.components.metagenomics.SplitAssembly(**kwargs)[source]¶

Bases: flowcraft.generator.process.Process

Component to filter metagenomic assemblies by contig size If the contig is larger than $param.size, it gets separated from the original assembly to continue the processes downstream of the pipeline.

This process is set with:

input_type: fasta

output_type: fasta

ptype: assembly filter

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