- AbstractAction
- AbstractBAM2SAMModule
- AbstractClusterTaskScheduler
- AbstractConcatInputStream
- AbstractEoulsanRuntime
- AbstractEoulsanRuntime.EoulsanExecMode
- AbstractExecutorInterpreter
- AbstractExpressionModule
- AbstractFilterAndMapReadsModule
- AbstractInfoAction
- AbstractMetadata
- AbstractModule
- AbstractParameterToolElement
- AbstractPort
- AbstractPorts
- AbstractReadsFilterModule
- AbstractReadsMapperModule
- AbstractRequirement
- AbstractResourceLoader
- AbstractRExecutor
- AbstractSAM2BAMModule
- AbstractSAM2FASTQModule
- AbstractSAMFilterModule
- AbstractSplice2BEDModule
- AbstractStep
- AbstractTaskScheduler
- AbstractToolElement
- AbstractWorkflow
- Action
- ActionService
- AdditionalAnnotationDataProtocol
- AnnotationDataProtocol
- ApacheCommonCompressionCodecs
- BAM2SAMLocalModule
- BAMMerger
- BAMSplitter
- BasicUI
- BedToolsModule
- BooleanParameterToolElement
- BpipeTaskScheduler
- BufferedHandler
- BundledScriptBpipeTaskScheduler
- ByteCountInputStream
- ByteCountOutputStream
- Checker
- CheckerModule
- CheckStore
- CheetahInterpreter
- ChIPSeqDataFormats
- ClassLoaderObjectInputStream
- ClassPathResourceLoader
- CLIMergingAnySAMOutputFormat
- ClusterCombinedTaskScheduler
- ClusterExecAction
- ClusterJobEmergencyStopTask
- ClusterTaskAction
- ClusterTaskScheduler
- ClusterTaskScheduler.StatusResult
- ClusterTaskScheduler.StatusValue
- ClusterTaskSchedulerService
- CollectionUtils
- CombinedTaskScheduler
- CommandStep
- CommandWorkflow
- CommandWorkflowModel
- CommandWorkflowParser
- CommandWorkflowParser.StepOutputPort
- Common
- CommonHadoop
- CompressedSplitFastqLineReader
- ConditionalToolElement
- ContextUtil
- ContextUtils
- CopyDesignAndWorkflowFilesToOutputModule
- CopyInputDataModule
- CopyOutputDataModule
- Counters
- CounterSequenceFile
- CountSplicedReadsModule
- CreateDesignAction
- CreateHadoopJarAction
- Data
- DataFile
- DataFileDataPath
- DataFileDistCp
- DataFileDistCp.DistCpMapper
- DataFileGenomeDescStorage
- DataFileGenomeIndexStorage
- DataFileGenomeMapperIndexer
- DataFileMetadata
- DataFiles
- DataFileStorage
- DataFormat
- DataFormatConverter
- DataFormatRegistry
- DataFormats
- DataList
- DataMetadata
- DataMetadataStorage
- DataProtocol
- DataProtocolService
- DataToolElement
- DataUtils
- DeepToolsModule
- DefaultDesignReader
- DefaultExecutorInterpreter
- DefineDataFormatToDownload
- DeprecatedDataProtocol
- DESeq2
- DESeq2.FitType
- DESeq2.SizeFactorsType
- DESeq2.StatisticTest
- DESeq2DesignChecker
- DESeq2Module
- Design
- DesignBuilder
- DesignFactory
- DesignFormatFinderInputStream
- DesignMetadata
- DesignMetadataImpl
- DesignModule
- DesignReader
- DesignUtils
- DesignWriter
- DiffAna
- DiffAna.DispersionFitType
- DiffAna.DispersionMethod
- DiffAna.DispersionSharingMode
- DiffAnaModule
- DiffanaResultsAnnotationModule
- DistCp
- DistCp.DuplicationException
- DistributedLock
- DistributedLocker
- DockerExecutorInterpreter
- DockerRequirement
- DockerRExecutor
- DummyGeneratorModule
- DummyTaskScheduler
- EmergencyStopTask
- EmergencyStopTasks
- EmptyFileQC
- EmptyToolElement
- Eoulsan1DesignReader
- Eoulsan1DesignWriter
- Eoulsan2DesignReader
- Eoulsan2DesignWriter
- EoulsanAnnotationUtils
- EoulsanDockerManager
- EoulsanError
- EoulsanException
- EoulsanITRuntimeException
- EoulsanLogger
- EoulsanRuntime
- EoulsanRuntimeException
- EoulsanTranslatorUtils
- ExecAction
- ExecFileLock
- ExecJarHadoopAction
- ExecLock
- ExecutionMode
- Executor
- ExecutorArguments
- ExecutorInterpreter
- Experiment
- ExperimentImpl
- ExperimentMetadata
- ExperimentSample
- ExperimentSampleImpl
- ExperimentSampleMetadata
- ExperimentSampleMetadataImpl
- ExpressionCounterCounter
- ExpressionCounterUtils
- ExpressionHadoopModule
- ExpressionInputPreprocessor
- ExpressionLocalModule
- ExpressionMapper
- ExpressionMerger
- ExpressionOutputFormat
- ExpressionRecordWriter
- ExpressionReducer
- ExpressionResultsAnnotationModule
- ExpressionSAMOutputMapper
- ExpressionSplitter
- ExpressionToMatrixModule
- FailModule
- FakeModule
- FastQCInputPreprocessor
- FastQCModule
- FastQCRuntimePatcher
- FastqInputFormat
- FastqLineRecordReader
- FastqMerger
- FastqOutputFormat
- FastqRecordReader
- FastqRecordWriter
- FastqSequenceFile
- FastqSplitter
- FeatureCountsInputPreprocessor
- FileCharsets
- FileConcatInputStream
- FileDataProtocol
- FileNaming
- FileNamingParsingRuntimeException
- FileResourceLoader
- FilterAndMapReadsHadoopModule
- FinalExpressionFeaturesCreator
- FirstModule
- FloatParameterToolElement
- FormatsAction
- FTPPathDataProtocol
- FTPURLDataProtocol
- GalaxyToolInterpreter
- GalaxyToolModule
- GalaxyToolXMLParserUtils
- Generator
- GenericExecutorInterpreter
- GenericStorageGeneratorModule
- GenomeChecker
- GenomeDataProtocol
- GenomeDescriptionCreator
- GenomeDescriptionGeneratorModule
- GenomeMapperIndexGeneratorModule
- GFFChecker
- GFFDataProtocol
- GFFFastaGeneratorModule
- Globals
- GTFChecker
- GTFDataProtocol
- HadoopBamUtils
- HadoopCompatible
- HadoopCompatibleTaskScheduler
- HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
- HadoopCompressionCodecs
- HadoopEoulsanRuntime
- HadoopExecAction
- HadoopInfo
- HadoopJarRepackager
- HadoopJobEmergencyStopTask
- HadoopMappingUtils
- HadoopOnly
- HadoopReporter
- HadoopReporterIncrementer
- HadoopUploadModule
- HDFSDataDownloadModule
- HDFSPathDataProtocol
- HTCondorTaskScheduler
- HTMLReportArchiveNeigborClass
- HTTPPathDataProtocol
- HTTPSPathDataProtocol
- HTTPSURLDataProtocol
- HTTPURLDataProtocol
- IDRModule
- ImportModule
- InfoAction
- Infos
- Infos.Info
- InputPort
- InputPorts
- InputPortsBuilder
- InputPreprocessor
- InputPreprocessorService
- IntegerParameterToolElement
- IntegrationTestAction
- JarRepack
- LanternaUI
- LinuxCpuInfo
- LinuxInfo
- LinuxMemInfo
- LocalEoulsanRuntime
- LocalOnly
- LocalUploadModule
- Locker
- LockerUtils
- MACS2Module
- Main
- MainCLI
- MainHadoop
- MapperIndexDataFormat
- MapperInputPreprocessor
- MappingCounters
- MapReduceUtils
- MatrixToCellRangerMatrixModule
- MaxByteInputStream
- MergeInputRepLocalModule
- MergePeaksModule
- Merger
- MergerModule
- Metadata
- Minimap2IndexGeneratorModule
- Module
- ModuleRegistry
- Modules
- ModulesAction
- ModuleService
- MonoThreadTaskScheduler
- MultiQCModule
- MultiThreadTaskScheduler
- Naming
- NoLog
- NoOutputDirectory
- Normalization
- NormalizationModule
- NoUI
- OtherLogConfigurator
- OutputPort
- OutputPorts
- OutputPortsBuilder
- PairedEndFastqToTfq
- PairedEndFastqToTfq.FastqPairedEndReducer
- ParallelizationMode
- Parameter
- PathConcatInputStream
- PathDataProtocol
- PathRequirement
- PathUtils
- PathUtils.PrefixPathFilter
- PathUtils.SuffixPathFilter
- PausableThreadPoolExecutor
- PBSProTaskScheduler
- Port
- Ports
- PreTreatmentExpressionMapper
- PreTreatmentExpressionReducer
- PreTreatmentMapper
- PreTreatmentReducer
- ProcessRExecutor
- ProcessUtils
- ProcessUtils.ProcessResult
- ProcessUtils.ProcessThreadErrOutput
- Progress
- ProgressCounterInputStream
- ProgressCounterOutputStream
- ReadsChecker
- ReadsFilterHadoopModule
- ReadsFilterLocalModule
- ReadsFilterMapper
- ReadsMapperHadoopModule
- ReadsMapperLocalModule
- ReadsMapperMapper
- Requirement
- RequirementInstallerModule
- RequirementService
- RequiresAllPreviousSteps
- RequiresPreviousStep
- ResourceLoader
- ReuseModuleInstance
- RExecutor
- RExecutorFactory
- RExecutorFactory.Mode
- RmDupLocalModule
- RModuleCommonConfiguration
- RSConnection
- RserveRequirement
- RserveRExecutor
- RSingleCellExperimentCreatorModule
- SAM2BAMHadoopModule
- SAM2BAMLocalModule
- SAM2FASTQLocalModule
- SAMFilterHadoopModule
- SAMFilterLocalModule
- SAMFilterMapper
- SAMFilterReducer
- SAMHeaderHadoopUtils
- SAMHeaderHadoopUtils.SAMHeaderWriter
- SAMInputFormat
- SAMMerger
- SAMOutputFormat
- Sample
- SampleMetadata
- SAMRecordReader
- SAMRecordWriter
- SAMSequenceFile
- SAMSplitter
- SelectParameterToolElement
- SerializableStopwatch
- Settings
- ShellModule
- SimpleInputPort
- SimpleInputPorts
- SimpleOutputPort
- SimpleOutputPorts
- SLURMTaskScheduler
- Splice2BEDModule
- Splitter
- SplitterModule
- STARIndexGeneratorModule
- Step
- Step.DiscardOutput
- Step.StepState
- Step.StepType
- StepConfigurationContext
- StepConfigurationContextImpl
- StepInstances
- StepObserver
- StepObserverRegistry
- StepOutputDataFile
- StepResult
- StepStateDependencies
- StepStatus
- StorageDataProtocol
- TaskContext
- TaskContextImpl
- TaskResult
- TaskResultImpl
- TaskRunner
- TaskScheduler
- TaskSchedulerFactory
- TaskSerializationUtils
- TaskStatus
- TaskStatusImpl
- TechnicalReplicateMergerModule
- Terminal
- TerminalModule
- TextParameterToolElement
- TGCCTaskScheduler
- Ticket
- TicketLocker
- TicketScheduler
- TicketSchedulerServer
- TokenManager
- TokenManagerRegistry
- ToolElement
- ToolElementFactory
- ToolExecutor
- ToolExecutorResult
- ToolInfo
- TORQUETaskScheduler
- TrackHubModule
- UI
- UIEvent
- UIService
- UIStepEvent
- UITaskEvent
- UIWorkflowEvent
- UnmodifiableData
- UnmodifiableExperiment
- UnmodifiableExperimentMetadata
- UnmodifiableExperimentSampleMetadata
- UploadModule
- URLDataProtocol
- Utils
- Workflow
- Workflow2Graphviz
- WorkflowContext
- WorkflowDataUtils
- WorkflowEventBus
- WorkflowFileNaming
- XMLDataFormat
- ZooKeeperLocker