Package fr.ens.biologie.genomique.eoulsan.modules

Class AbstractModule

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
All Implemented Interfaces:
Module
Direct Known Subclasses:
AbstractBAM2SAMModule, AbstractExpressionModule, AbstractFilterAndMapReadsModule, AbstractReadsFilterModule, AbstractReadsMapperModule, AbstractSAM2BAMModule, AbstractSAM2FASTQModule, AbstractSAMFilterModule, AbstractSplice2BEDModule, BedToolsModule, CheckerModule, CopyDesignAndWorkflowFilesToOutputModule, CopyInputDataModule, CopyOutputDataModule, CountSplicedReadsModule, DeepToolsModule, DefineDataFormatToDownload, DESeq2Module, DesignModule, DiffAnaModule, DiffanaResultsAnnotationModule, DummyGeneratorModule, ExpressionResultsAnnotationModule, ExpressionToMatrixModule, FailModule, FakeModule, FastQCModule, FirstModule, GalaxyToolModule, GenericStorageGeneratorModule, GenomeDescriptionGeneratorModule, GenomeMapperIndexGeneratorModule, GFFFastaGeneratorModule, HDFSDataDownloadModule, IDRModule, ImportModule, MACS2Module, MatrixToCellRangerMatrixModule, MergeInputRepLocalModule, MergePeaksModule, MergerModule, Minimap2IndexGeneratorModule, MultiQCModule, NormalizationModule, RequirementInstallerModule, RmDupLocalModule, RSingleCellExperimentCreatorModule, ShellModule, SplitReadsModule, SplitterModule, STARIndexGeneratorModule, TerminalModule, TrackHubModule, UploadModule
public abstract class AbstractModule extends Object implements Module
This class define an abstract Module.
Since:
1.0
Author:
Laurent Jourdren

  • Constructor Details

    • AbstractModule

      public AbstractModule()

  • Method Details

    • getDescription

      public String getDescription()
      Description copied from interface: Module
      Get the description of the module
      Specified by:
      getDescription in interface Module
      Returns:
      the description of the module

    • getRequiredEoulsanVersion

      public fr.ens.biologie.genomique.kenetre.util.Version getRequiredEoulsanVersion()
      Description copied from interface: Module
      Get the required Version of the application to run the Module.
      Specified by:
      getRequiredEoulsanVersion in interface Module
      Returns:
      a Version object with the required version of the Module

    • getInputPorts

      public InputPorts getInputPorts()
      Description copied from interface: Module
      Get the input data format.
      Specified by:
      getInputPorts in interface Module
      Returns:
      a set with DataFormat or null if the module does not any need input format

    • getOutputPorts

      public OutputPorts getOutputPorts()
      Description copied from interface: Module
      Get the output data format.
      Specified by:
      getOutputPorts in interface Module
      Returns:
      an set with DataFormat or null if the module does not produce any output data

    • getRequirements

      public Set<Requirement> getRequirements()
      Description copied from interface: Module
      Get the requirements of the module.
      Specified by:
      getRequirements in interface Module
      Returns:
      a set with the requirements of the module

    • getChecker

      public Checker getChecker()
      Description copied from interface: Module
      Get the checker for the module
      Specified by:
      getChecker in interface Module
      Returns:
      the checker for the module

    • configure

      public void configure(StepConfigurationContext context, Set<Parameter> stepParameters) throws EoulsanException
      Description copied from interface: Module
      Set the parameters of the step to configure the module.
      Specified by:
      configure in interface 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

    • getParallelizationMode

      public ParallelizationMode getParallelizationMode()
      Description copied from interface: Module
      Get the parallelization mode of the module.
      Specified by:
      getParallelizationMode in interface Module
      Returns:
      a ParallelizationMode enum