flowcraft.generator.components.reads_quality_control module

class flowcraft.generator.components.reads_quality_control.IntegrityCoverage(**kwargs)

Bases: flowcraft.generator.process.Process

Process template interface for first integrity_coverage process

This process is set with:

• input_type: fastq
• output_type: fastq
• ptype: pre_assembly

It contains two secondary channel link starts:

• SIDE_phred: Phred score of the FastQ files
• SIDE_max_len: Maximum 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.reads_quality_control.CheckCoverage(**kwargs)

Bases: flowcraft.generator.process.Process

Process template interface for additional integrity_coverage process

This process is set with:

• input_type: fastq
• output_type: fastq
• ptype: pre_assembly

It contains one secondary channel link start:

• SIDE_max_len: Maximum 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.reads_quality_control.TrueCoverage(**kwargs)

Bases: flowcraft.generator.process.Process

TrueCoverage 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

class flowcraft.generator.components.reads_quality_control.Fastqc(**kwargs)

Bases: flowcraft.generator.process.Process

FastQC process template interface

This process is set with:

• input_type: fastq
• output_type: fastq
• ptype: pre_assembly

It contains two status channels:

• STATUS_fastqc: Status for the fastqc process
• STATUS_report: Status for the fastqc_report 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

status_channels = None

list: Setting status channels for FastQC execution and FastQC report

class flowcraft.generator.components.reads_quality_control.Trimmomatic(**kwargs)

Bases: flowcraft.generator.process.Process

Trimmomatic process template interface

This process is set with:

• input_type: fastq
• output_type: fastq
• ptype: pre_assembly

It contains one secondary channel link end:

• SIDE_phred (alias: SIDE_phred): Receives FastQ phred score

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.reads_quality_control.FastqcTrimmomatic(**kwargs)

Bases: flowcraft.generator.process.Process

Fastqc + Trimmomatic process template interface

This process executes FastQC only to inform the trim range for trimmomatic, not for QC checks.

This process is set with:

• input_type: fastq
• output_type: fastq
• ptype: pre_assembly

It contains one secondary channel link end:

• SIDE_phred (alias: SIDE_phred): Receives FastQ phred score

It contains three status channels:

• STATUS_fastqc: Status for the fastqc process
• STATUS_report: Status for the fastqc_report process
• STATUS_trim: Status for the trimmomatic 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

class flowcraft.generator.components.reads_quality_control.FilterPoly(**kwargs)

Bases: flowcraft.generator.process.Process

PrinSeq process to filter non-informative sequences from reads

This process is set with:

• input_type: fastq
• output_type: fastq
• ptype: pre_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

class flowcraft.generator.components.reads_quality_control.DownsampleFastq(**kwargs)

Bases: flowcraft.generator.process.Process

Downsamples FastQ file based on depth using seqtk

This process is set with:

• input_type: fastq
• output_type: fastq

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