Uses of Interface
fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext

Packages that use StepConfigurationContext

Package	Description
fr.ens.biologie.genomique.eoulsan.core	This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.workflow	This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.modules	This package define the steps for the Eoulsan workflow.
fr.ens.biologie.genomique.eoulsan.modules.chipseq	This packages contains the ChIP-Seq modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling	This packages contains the peak-calling modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc	This packages contains all the quality check modules for ChIP-Seq.
fr.ens.biologie.genomique.eoulsan.modules.diffana	This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.modules.expression	This package contain all the classes related to the expression step.
fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop	This package contain all the classes related to the expression step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.fastqc	This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators	This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mapping.local	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop	This package contain classes related data management in Hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload	This package contain classes related to upload data to HDFS and Cloud.
fr.ens.biologie.genomique.eoulsan.modules.multiqc
fr.ens.biologie.genomique.eoulsan.modules.singlecell

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.core

Subinterfaces of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.core

Modifier and Type	Interface	Description
interface	TaskContext	This interface define the context of a step.

Methods in fr.ens.biologie.genomique.eoulsan.core with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
static void	Modules.badParameterValue(StepConfigurationContext context, Parameter parameter, String message)	Throw a exception for bad parameter value.
void	Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
static void	Modules.deprecatedParameter(StepConfigurationContext context, Parameter parameter)	Show a message for deprecated parameters.
static void	Modules.deprecatedParameter(StepConfigurationContext context, Parameter parameter, boolean throwException)	Show a message for deprecated parameters.
static void	Modules.invalidConfiguration(StepConfigurationContext context, String message)	Throw a exception for an invalid configuration.
static void	Modules.removedParameter(StepConfigurationContext context, Parameter parameter)	Throw a exception for removed parameters.
static void	Modules.renamedParameter(StepConfigurationContext context, Parameter parameter, String newParameterName)	Show a message for deprecated parameters that has been renamed.
static void	Modules.renamedParameter(StepConfigurationContext context, Parameter parameter, String newParameterName, boolean throwException)	Show a message for deprecated parameters that has been renamed.
static void	Modules.unknownParameter(StepConfigurationContext context, Parameter parameter)	Throw a exception for unknown parameters.

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.core.workflow

Classes in fr.ens.biologie.genomique.eoulsan.core.workflow that implement StepConfigurationContext

Modifier and Type	Class	Description
class	StepConfigurationContextImpl	This class define a concrete implementation of the configuration context of a step.
class	TaskContextImpl	This class define a task context.

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules

Methods in fr.ens.biologie.genomique.eoulsan.modules with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	AbstractModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	CopyInputDataModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	CopyOutputDataModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DesignModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	FailModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	FakeModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	GalaxyToolModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ImportModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	MergerModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	RequirementInstallerModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ShellModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	SplitterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.chipseq

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	MergeInputRepLocalModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	RmDupLocalModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	TrackHubModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	BedToolsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	DeepToolsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	MACS2Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	MergePeaksModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	CountSplicedReadsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	IDRModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set IDR parameters to configure the step.

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.diffana

Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	DESeq2Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DiffAnaModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DiffanaResultsAnnotationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	NormalizationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
static RExecutor	RModuleCommonConfiguration.parseRExecutorParameter(StepConfigurationContext context, Set<Parameter> stepParameters, Set<Requirement> requirements, String defaultDockerImage)	Parse the step parameter and create a configured RExecutor object.

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.expression

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	AbstractExpressionModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ExpressionResultsAnnotationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	ExpressionHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.fastqc

Methods in fr.ens.biologie.genomique.eoulsan.modules.fastqc with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	FastQCModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.generators

Methods in fr.ens.biologie.genomique.eoulsan.modules.generators with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	GenericStorageGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	GenomeMapperIndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	Minimap2IndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	STARIndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mapping

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	AbstractBAM2SAMModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractFilterAndMapReadsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractReadsFilterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractReadsMapperModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAM2BAMModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAM2FASTQModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAMFilterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSplice2BEDModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	FilterAndMapReadsHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ReadsMapperHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mapping.local

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.local with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	SplitReadsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	CopyDesignAndWorkflowFilesToOutputModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	DefineDataFormatToDownload.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	HDFSDataDownloadModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.multiqc

Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	MultiQCModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.singlecell

Methods in fr.ens.biologie.genomique.eoulsan.modules.singlecell with parameters of type StepConfigurationContext

Modifier and Type	Method	Description
void	ExpressionToMatrixModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	MatrixToCellRangerMatrixModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	RSingleCellExperimentCreatorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)