flowcraft.generator.components.reads_quality_control module¶
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class
flowcraft.generator.components.reads_quality_control.
IntegrityCoverage
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Process template interface for first integrity_coverage process
This process is set with:
input_type
: fastqoutput_type
: fastqptype
: pre_assembly
It contains two secondary channel link starts:
SIDE_phred
: Phred score of the FastQ filesSIDE_max_len
: Maximum 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
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class
flowcraft.generator.components.reads_quality_control.
CheckCoverage
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Process template interface for additional integrity_coverage process
This process is set with:
input_type
: fastqoutput_type
: fastqptype
: 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
(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
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class
flowcraft.generator.components.reads_quality_control.
TrueCoverage
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
TrueCoverage process template interface
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
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class
flowcraft.generator.components.reads_quality_control.
Fastqc
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
FastQC process template interface
This process is set with:
input_type
: fastqoutput_type
: fastqptype
: pre_assembly
It contains two status channels:
STATUS_fastqc
: Status for the fastqc processSTATUS_report
: Status for the fastqc_report 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 -
status_channels
= None¶ list: Setting status channels for FastQC execution and FastQC report
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class
flowcraft.generator.components.reads_quality_control.
Trimmomatic
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Trimmomatic process template interface
This process is set with:
input_type
: fastqoutput_type
: fastqptype
: 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
(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
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class
flowcraft.generator.components.reads_quality_control.
FastqcTrimmomatic
(**kwargs)[source]¶ 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
: fastqoutput_type
: fastqptype
: 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 processSTATUS_report
: Status for the fastqc_report processSTATUS_trim
: Status for the trimmomatic 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
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class
flowcraft.generator.components.reads_quality_control.
FilterPoly
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
PrinSeq process to filter non-informative sequences from reads
This process is set with:
input_type
: fastqoutput_type
: fastqptype
: pre_assembly
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
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class
flowcraft.generator.components.reads_quality_control.
DownsampleFastq
(**kwargs)[source]¶ Bases:
flowcraft.generator.process.Process
Downsamples FastQ file based on depth using seqtk
This process is set with:
input_type
: fastqoutput_type
: fastq
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