flowcraft.generator.components.metagenomics module

class flowcraft.generator.components.metagenomics.Concoct(**kwargs)

Bases: flowcraft.generator.process.Process

CONCOCT process template interface for the taxonomic independent binning of metagenomic assemblies.

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(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.metagenomics.Kraken(**kwargs)

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(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.metagenomics.Kraken2(**kwargs)

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(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.metagenomics.Maxbin2(**kwargs)

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(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.metagenomics.Megahit(**kwargs)

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(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.metagenomics.Metabat2(**kwargs)

Bases: flowcraft.generator.process.Process

MetaBat2 process template interface for the taxonomic independent binning of metagenomic assemblies.

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.metagenomics.Metaspades(**kwargs)

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(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.metagenomics.Midas_species(**kwargs)

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(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.metagenomics.RemoveHost(**kwargs)

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(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.metagenomics.Metaprob(**kwargs)

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(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.metagenomics.SplitAssembly(**kwargs)

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(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