Package fr.ens.biologie.genomique.eoulsan.core

Interface Module

All Known Implementing Classes:

AbstractBAM2SAMModule, AbstractExpressionModule, AbstractFilterAndMapReadsModule, AbstractModule, AbstractReadsFilterModule, AbstractReadsMapperModule, AbstractSAM2BAMModule, AbstractSAM2FASTQModule, AbstractSAMFilterModule, AbstractSplice2BEDModule, BAM2SAMLocalModule, BedToolsModule, CheckerModule, CopyDesignAndWorkflowFilesToOutputModule, CopyInputDataModule, CopyOutputDataModule, CountSplicedReadsModule, DeepToolsModule, DefineDataFormatToDownload, DESeq2Module, DesignModule, DiffAnaModule, DiffanaResultsAnnotationModule, DummyGeneratorModule, ExpressionHadoopModule, ExpressionLocalModule, ExpressionResultsAnnotationModule, ExpressionToMatrixModule, FailModule, FakeModule, FastQCModule, FilterAndMapReadsHadoopModule, FirstModule, GalaxyToolModule, GenericStorageGeneratorModule, GenomeDescriptionGeneratorModule, GenomeMapperIndexGeneratorModule, GFFFastaGeneratorModule, HadoopUploadModule, HDFSDataDownloadModule, IDRModule, ImportModule, LocalUploadModule, MACS2Module, MatrixToCellRangerMatrixModule, MergeInputRepLocalModule, MergePeaksModule, MergerModule, Minimap2IndexGeneratorModule, MultiQCModule, NormalizationModule, ReadsFilterHadoopModule, ReadsFilterLocalModule, ReadsMapperHadoopModule, ReadsMapperLocalModule, RequirementInstallerModule, RmDupLocalModule, RSingleCellExperimentCreatorModule, SAM2BAMHadoopModule, SAM2BAMLocalModule, SAM2FASTQLocalModule, SAMFilterHadoopModule, SAMFilterLocalModule, ShellModule, Splice2BEDModule, SplitterModule, STARIndexGeneratorModule, TechnicalReplicateMergerModule, TerminalModule, TrackHubModule, UploadModule

public interface Module

This interface define a Module.

Since:

1.0

Author:

Laurent Jourdren

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.
Checker	getChecker()	Get the checker for the module
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.
ParallelizationMode	getParallelizationMode()	Get the parallelization mode of the module.
fr.ens.biologie.genomique.kenetre.util.Version	getRequiredEoulsanVersion()	Get the required Version of the application to run the Module.
Set<Requirement>	getRequirements()	Get the requirements of the module.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

Method Detail

getName

String getName()

Get the name of the module.

Returns:

the name of the module

getDescription

String getDescription()

Get the description of the module

Returns:

the description of the module

getVersion

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

Get version of the Module.

Returns:

a Version object with the version of the Module

getRequiredEoulsanVersion

fr.ens.biologie.genomique.kenetre.util.Version getRequiredEoulsanVersion()

Get the required Version of the application to run the Module.

Returns:

a Version object with the required version of the Module

getInputPorts

InputPorts getInputPorts()

Get the input data format.

Returns:

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

getOutputPorts

OutputPorts getOutputPorts()

Get the output data format.

Returns:

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

getRequirements

Set<Requirement> getRequirements()

Get the requirements of the module.

Returns:

a set with the requirements of the module

getChecker

Checker getChecker()

Get the checker for the module

Returns:

the checker for the module

configure

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

Set the parameters of the step to configure the module.

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

TaskResult execute(TaskContext context,
                   TaskStatus status)

Execute a task step.

Parameters:

context - Execution context

status - of the task

getParallelizationMode

ParallelizationMode getParallelizationMode()

Get the parallelization mode of the module.

Returns:

a ParallelizationMode enum