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

Packages that use OutputPorts

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.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.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.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 OutputPorts in fr.ens.biologie.genomique.eoulsan.core

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

Modifier and Type	Class	Description
class	SimpleOutputPorts	This class define a class that contains several output ports.

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

Modifier and Type	Method	Description
static OutputPorts	OutputPortsBuilder.copy(OutputPorts ports)	Convenient method to create a defensive copy of an OutputPorts object.
OutputPorts	OutputPortsBuilder.create()	Create the ports.
OutputPorts	Module.getOutputPorts()	Get the output data format.
OutputPorts	Step.getOutputPorts()	Get the output ports of the step.
static OutputPorts	OutputPortsBuilder.noOutputPort()	Create the ports with no ports.
static OutputPorts	OutputPortsBuilder.singleOutputPort(DataFormat format)	Convenient method to create the ports with only one port.
static OutputPorts	OutputPortsBuilder.singleOutputPort(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 OutputPorts

Modifier and Type	Method	Description
static OutputPorts	OutputPortsBuilder.copy(OutputPorts ports)	Convenient method to create a defensive copy of an OutputPorts object.

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

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

Modifier and Type	Method	Description
OutputPorts	AbstractStep.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	AbstractModule.getOutputPorts()
OutputPorts	CopyInputDataModule.getOutputPorts()
OutputPorts	CopyOutputDataModule.getOutputPorts()
OutputPorts	DesignModule.getOutputPorts()
OutputPorts	GalaxyToolModule.getOutputPorts()
OutputPorts	ImportModule.getOutputPorts()
OutputPorts	MergerModule.getOutputPorts()
OutputPorts	SplitterModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	MergeInputRepLocalModule.getOutputPorts()	Define output port.
OutputPorts	RmDupLocalModule.getOutputPorts()	Define output port.

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

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

Modifier and Type	Method	Description
OutputPorts	BedToolsModule.getOutputPorts()
OutputPorts	MACS2Module.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	DiffanaResultsAnnotationModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	AbstractExpressionModule.getOutputPorts()
OutputPorts	ExpressionResultsAnnotationModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	FastQCModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	DummyGeneratorModule.getOutputPorts()
OutputPorts	GenericStorageGeneratorModule.getOutputPorts()
OutputPorts	GenomeDescriptionGeneratorModule.getOutputPorts()
OutputPorts	GenomeMapperIndexGeneratorModule.getOutputPorts()
OutputPorts	GFFFastaGeneratorModule.getOutputPorts()
OutputPorts	Minimap2IndexGeneratorModule.getOutputPorts()
OutputPorts	STARIndexGeneratorModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	AbstractBAM2SAMModule.getOutputPorts()
OutputPorts	AbstractFilterAndMapReadsModule.getOutputPorts()
OutputPorts	AbstractReadsFilterModule.getOutputPorts()
OutputPorts	AbstractReadsMapperModule.getOutputPorts()
OutputPorts	AbstractSAM2BAMModule.getOutputPorts()
OutputPorts	AbstractSAM2FASTQModule.getOutputPorts()
OutputPorts	AbstractSAMFilterModule.getOutputPorts()
OutputPorts	AbstractSplice2BEDModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	ReadsMapperLocalModule.getOutputPorts()
OutputPorts	SplitReadsModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	MultiQCModule.getOutputPorts()

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

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

Modifier and Type	Method	Description
OutputPorts	ExpressionToMatrixModule.getOutputPorts()
OutputPorts	MatrixToCellRangerMatrixModule.getOutputPorts()
OutputPorts	RSingleCellExperimentCreatorModule.getOutputPorts()