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, SplitReadsModule, SplitterModule, STARIndexGeneratorModule, TechnicalReplicateMergerModule, TerminalModule, TrackHubModule, UploadModule
public interface Module
This interface define a Module.
Since:
1.0
Author:
Laurent Jourdren

  • Method Details

    • 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
      Returns:
      a TaskResult object

    • getParallelizationMode

      ParallelizationMode getParallelizationMode()
      Get the parallelization mode of the module.
      Returns:
      a ParallelizationMode enum