Uses of Interface
fr.ens.biologie.genomique.eoulsan.core.OutputPorts
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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 -
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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()
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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()
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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()
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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()
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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()
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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()
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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()
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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()
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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()
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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()
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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()
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