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

Packages that use InputPorts

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.multiqc
fr.ens.biologie.genomique.eoulsan.modules.singlecell

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

Classes in fr.ens.biologie.genomique.eoulsan.core that implement InputPorts

Modifier and Type	Class	Description
class	SimpleInputPorts	This class define a class that handles a set of input ports.

Methods in fr.ens.biologie.genomique.eoulsan.core that return InputPorts

Modifier and Type	Method	Description
static InputPorts	InputPortsBuilder.allPortsRequiredInWorkingDirectory(InputPorts inputPorts)	Set all ports of an existing input ports to be required in working directory.
static InputPorts	InputPortsBuilder.copy(InputPorts ports)	Convenient method to create a defensive copy of an InputPorts object.
InputPorts	InputPortsBuilder.create()	Create the ports.
InputPorts	Module.getInputPorts()	Get the input data format.
InputPorts	Step.getInputPorts()	Get the input ports of the step.
static InputPorts	InputPortsBuilder.noInputPort()	Create the ports with no ports.
static InputPorts	InputPortsBuilder.singleInputPort(DataFormat format)	Convenient method to create the ports with only one port.
static InputPorts	InputPortsBuilder.singleInputPort(String name, DataFormat format)	Convenient method to create the ports with only one port.

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

Modifier and Type	Method	Description
static InputPorts	InputPortsBuilder.allPortsRequiredInWorkingDirectory(InputPorts inputPorts)	Set all ports of an existing input ports to be required in working directory.
static InputPorts	InputPortsBuilder.copy(InputPorts ports)	Convenient method to create a defensive copy of an InputPorts object.

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

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return InputPorts

Modifier and Type	Method	Description
InputPorts	AbstractStep.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules that return InputPorts

Modifier and Type	Method	Description
InputPorts	AbstractModule.getInputPorts()
InputPorts	CheckerModule.getInputPorts()
InputPorts	CopyInputDataModule.getInputPorts()
InputPorts	CopyOutputDataModule.getInputPorts()
InputPorts	FailModule.getInputPorts()
InputPorts	GalaxyToolModule.getInputPorts()
InputPorts	MergerModule.getInputPorts()
InputPorts	SplitterModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq that return InputPorts

Modifier and Type	Method	Description
InputPorts	MergeInputRepLocalModule.getInputPorts()	Define input port.
InputPorts	RmDupLocalModule.getInputPorts()	Define input port.
InputPorts	TrackHubModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling that return InputPorts

Modifier and Type	Method	Description
InputPorts	BedToolsModule.getInputPorts()
InputPorts	DeepToolsModule.getInputPorts()
InputPorts	MACS2Module.getInputPorts()
InputPorts	MergePeaksModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc that return InputPorts

Modifier and Type	Method	Description
InputPorts	CountSplicedReadsModule.getInputPorts()	Define input ports.
InputPorts	IDRModule.getInputPorts()	Define input ports.

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana that return InputPorts

Modifier and Type	Method	Description
InputPorts	DESeq2Module.getInputPorts()
InputPorts	DiffAnaModule.getInputPorts()
InputPorts	DiffanaResultsAnnotationModule.getInputPorts()
InputPorts	NormalizationModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression that return InputPorts

Modifier and Type	Method	Description
InputPorts	AbstractExpressionModule.getInputPorts()
InputPorts	ExpressionResultsAnnotationModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop that return InputPorts

Modifier and Type	Method	Description
InputPorts	ExpressionHadoopModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.fastqc that return InputPorts

Modifier and Type	Method	Description
InputPorts	FastQCModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.generators that return InputPorts

Modifier and Type	Method	Description
InputPorts	GenericStorageGeneratorModule.getInputPorts()
InputPorts	GenomeDescriptionGeneratorModule.getInputPorts()
InputPorts	GenomeMapperIndexGeneratorModule.getInputPorts()
InputPorts	GFFFastaGeneratorModule.getInputPorts()
InputPorts	Minimap2IndexGeneratorModule.getInputPorts()
InputPorts	STARIndexGeneratorModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping that return InputPorts

Modifier and Type	Method	Description
InputPorts	AbstractBAM2SAMModule.getInputPorts()
InputPorts	AbstractFilterAndMapReadsModule.getInputPorts()
InputPorts	AbstractReadsFilterModule.getInputPorts()
InputPorts	AbstractSAM2BAMModule.getInputPorts()
InputPorts	AbstractSAM2FASTQModule.getInputPorts()
InputPorts	AbstractSAMFilterModule.getInputPorts()
InputPorts	AbstractSplice2BEDModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop that return InputPorts

Modifier and Type	Method	Description
InputPorts	FilterAndMapReadsHadoopModule.getInputPorts()
InputPorts	ReadsFilterHadoopModule.getInputPorts()
InputPorts	ReadsMapperHadoopModule.getInputPorts()
InputPorts	SAM2BAMHadoopModule.getInputPorts()
InputPorts	SAMFilterHadoopModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.local that return InputPorts

Modifier and Type	Method	Description
InputPorts	ReadsMapperLocalModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc that return InputPorts

Modifier and Type	Method	Description
InputPorts	MultiQCModule.getInputPorts()

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.singlecell that return InputPorts

Modifier and Type	Method	Description
InputPorts	ExpressionToMatrixModule.getInputPorts()
InputPorts	MatrixToCellRangerMatrixModule.getInputPorts()
InputPorts	RSingleCellExperimentCreatorModule.getInputPorts()