Package fr.ens.biologie.genomique.eoulsan.modules.fastqc

Class FastQCModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule

All Implemented Interfaces:

Module

public class FastQCModule
extends AbstractModule

This class define a module that compute QC report using FastQC.

Since:

2.0

Author:

Sandrine Perrin

Field Summary

Fields

Modifier and Type	Field	Description
static String	FASTQC_CASAVA_PARAMETER_NAME	Format fastq type casava/Illumina
static String	FASTQC_EXPGROUP_PARAMETER_NAME	Use exponential base groups in graph
static String	FASTQC_KMER_SIZE_PARAMETER_NAME	Collector FastQC kmer size
static String	FASTQC_NOFILTER_PARAMETER_NAME	Option for filter fastq file if casava=true for all modules
static String	FASTQC_NOGROUP_PARAMETER_NAME	Collector FastQC nogroup

Constructor Summary

Constructors

Constructor	Description
FastQCModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
String	getDescription()	Get the description of the module
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
OutputPorts	getOutputPorts()	Get the output data format.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FASTQC_KMER_SIZE_PARAMETER_NAME

public static final String FASTQC_KMER_SIZE_PARAMETER_NAME

Collector FastQC kmer size

See Also:

Constant Field Values

FASTQC_NOGROUP_PARAMETER_NAME

public static final String FASTQC_NOGROUP_PARAMETER_NAME

Collector FastQC nogroup

See Also:

Constant Field Values

FASTQC_EXPGROUP_PARAMETER_NAME

public static final String FASTQC_EXPGROUP_PARAMETER_NAME

Use exponential base groups in graph

See Also:

Constant Field Values

FASTQC_CASAVA_PARAMETER_NAME

public static final String FASTQC_CASAVA_PARAMETER_NAME

Format fastq type casava/Illumina

See Also:

Constant Field Values

FASTQC_NOFILTER_PARAMETER_NAME

public static final String FASTQC_NOFILTER_PARAMETER_NAME

Option for filter fastq file if casava=true for all modules

See Also:

Constant Field Values

Constructor Detail

FastQCModule

public FastQCModule()

Method Detail

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getDescription

public String getDescription()

Description copied from interface: Module

Get the description of the module

Specified by:

getDescription in interface Module

Overrides:

getDescription in class AbstractModule

Returns:

the description of the module

getVersion

public fr.ens.biologie.genomique.kenetre.util.Version getVersion()

Description copied from interface: Module

Get version of the Module.

Returns:

a Version object with the version of the Module

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

a set with DataFormat or null if the module does not any need input format

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractModule

Returns:

an set with DataFormat or null if the module does not produce any output data

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task