All Classes and Interfaces

Class	Description
AbstractAction	This class define an abstract Action
AbstractBAM2SAMModule	This class define a module for converting BAM files into SAM.
AbstractClusterTaskScheduler	This class is a scheduler for task running on a cluster.
AbstractClusterTaskScheduler.ProcessThreadOutput	This class allow to fetch standard output or standard error.
AbstractConcatInputStream	This class define an InputStream that concatenate InputStream.
AbstractEasyContrasts	This class contains methods to run the differential analysis module DESeq2.
AbstractEoulsanRuntime	This class define an abstract EoulsanRuntime.
AbstractEoulsanRuntime.EoulsanExecMode	This Enum define the Eoulsan execution mode.
AbstractExecutorInterpreter	This class define an abstract executor interpreter that contains the default implementation of the execute() method that use a ProcessBuilder.
AbstractExpressionModule	This abstract class define and parse arguments for the expression module.
AbstractFilterAndMapReadsModule	This class define an abstract module for read filtering, mapping and alignments filtering.
AbstractInfoAction	This class define an abstract action that show the some Eoulsan configuration and available modules
AbstractMetadata	This abstract class defines methods for metadata.
AbstractModule	This class define an abstract Module.
AbstractParameterToolElement	This class define an abstract class for tool element parameters.
AbstractPort	Abstract class that define a port.
AbstractPorts<E extends Port>	This class define a basic implementation of a Ports class.
AbstractReadsFilterModule	This class define an abstract module for read filtering.
AbstractReadsMapperModule	This class define an abstract module for read mapping.
AbstractRequirement	This class define an abstract requirement.
AbstractResourceLoader<S>	This class define an abstract resource loader.
AbstractRExecutor	This class define an abstract RExecutor.
AbstractSAM2BAMModule	This class define a module for converting SAM files into BAM.
AbstractSAM2FASTQModule	This class define a module for converting SAM files into BAM.
AbstractSAMFilterModule	This class define an abstract module for alignments filtering.
AbstractSplice2BEDModule	This class define a module for converting SAM files into BED.
AbstractStep	This class define a step of the workflow.
AbstractTaskScheduler	This class define an abstract task scheduler.
AbstractToolElement	This class define an abstract tool element.
AbstractWorkflow	This class define a Workflow.
Action	This interface define an action.
ActionService	This class define a service to retrieve an Action
AdditionalAnnotationDataProtocol	This class define a additional annotation protocol.
AnnotationDataProtocol	This class define a annotation protocol.
ApacheCommonCompressionCodecs	This class allow to create input and output stream for compression codecs of the Apache Common Compression library.
BAM2SAMLocalModule	This class define a module for converting BAM files into SAM.
BAMMerger	This class define a merger class for SAM files.
BAMSplitter	This class define a splitter class for BAM files.
BasicUI	This class define a basic UI for Eoulsan.
BedToolsModule	This class uses tools from the BEDTools suite.
BooleanParameterToolElement	This class define a boolean tool element parameter.
BpipeTaskScheduler	This class allow to submit, stop and get the status of jobs using Bpipe scheduler wrappers.
BufferedHandler	This class define a buffered handler.
BundledScriptBpipeTaskScheduler	This class define an abstract scheduler that use a bpipe script bundled in Eoulsan distribution.
ByteCountInputStream	This filter class allow to count the number of bytes read by an inputStream.
ByteCountOutputStream	This class define a filter that count the number of written bytes by an InputStream.
Checker	This interface define a checker.
CheckerModule	This class is a module that launch checkers.
CheckStore	This class define a storage where some results of the checker can be save for later reuse by other checkers.
CheetahInterpreter	This class create a Cheetah interpreter, it can build a command line tool from command tag from Galaxy tool XML file.
ChIPSeqDataFormats	This class contains the definition of some DataFormats for ChiP-Seq.
ClassLoaderObjectInputStream	This class allow to use ObjectInputStream with a ClassLoader that is not the default bootstrap ClassLoader.
ClassPathResourceLoader<S>	This class allow to define a resource loader for resources in the class path.
CLIMergingAnySAMOutputFormat<K>	Like a KeyIgnoringAnySAMOutputFormat, but sets the SAMFileHeader to Utils.getSAMHeaderMerger().getMergedHeader() and allows the output directory (the "work directory") to exist.
ClusterCombinedTaskScheduler	This class defined a combined task scheduler for cluster mode.
ClusterExecAction	This class define the cluster exec Action.
ClusterJobEmergencyStopTask	This class define an EmergencyStopTask for cluster Jobs.
ClusterTaskAction	This class define a action to launch a task on a cluster.
ClusterTaskScheduler	This interface define a cluster task scheduler.
ClusterTaskScheduler.StatusResult	This class define a Status result return by the statusJob() method of the interface.
ClusterTaskScheduler.StatusValue	This enum define the values of the status of a job.
ClusterTaskSchedulerService	This class define a service to retrieve a ClusterTaskScheduler.
CollectionUtils	This class define an utility class that contains useful methods for collections.
CombinedTaskScheduler	This class defined a combined task scheduler that use several context schedulers according to the parallelization mode of the step.
CommandStep	This class define a step based on a Command object (workflow file).
CommandWorkflow	This class define a workflow based on a Command object (workflow file).
CommandWorkflowModel	This class define the workflow model object of Eoulsan.
CommandWorkflowParser	This class allow parse the workflow file.
CommandWorkflowParser.StepOutputPort	Define a step output port.
Common	This class define common constants.
CommonHadoop	This class define common constants and other methods specific to Hadoop mode.
CompressedSplitFastqLineReader	This class define a split line reader for compressed FASTQ files.
ConditionalToolElement	This class define a conditional tool element.
ContextUtil	Utility methods to allow applications to deal with inconsistencies between MapReduce Context Objects API between hadoop-0.20 and later versions.
ContextUtils	This class define utility methods on Context.
CopyDesignAndWorkflowFilesToOutputModule	This module copy design and workflow file to output directory.
CopyInputDataModule	Copy input files of a format in another location or in different compression format.
CopyOutputDataModule	Copy output files of a step with a specified format to the output directory.
Counters	This class define the counters names used in this package.
CounterSequenceFile	This interface extends SequenceFile to add a getCount() method that allow to get the count of the read entries.
CountSplicedReadsModule	This step computes how many spliced alignments there are in a SAM file.
CreateDesignAction	This class define an action to create design file.
CreateHadoopJarAction	This class define an action to create hadoop jar file.
CutAdaptInputPreprocessor	This class define a preprocessor for Cutadapt reports.
Data	This interface define data used by ports.
DataFile	This class define a DataFile.
DataFileDataPath	This class define a bridge between Kenetre DataPath objects and Eoulsan DataFile objects.
DataFileDistCp	This class allow to copy and transform data in a distributed manner.
DataFileDistCp.DistCpMapper	This inner class define the mapper class for DataSourceDistCp map-reduce job.
DataFileGenomeDescStorage	This class define a storage for genome description files using DataFile API.
DataFileGenomeIndexStorage	This class define a storage for genome indexes using DataFile API.
DataFileGenomeMapperIndexer	This class define a genome mapper indexer.
DataFileMetadata	This class define source metadata
DataFiles	This class contains utility methods on DataFile objects.
DataFileStorage	This class define a storage using DataFile API.
DataFormat	This interface define a DataFormat.
DataFormatConverter	This class allow to copy and transform data while copying.
DataFormatRegistry	this class register DataFormat to allow get the DataFormat of a file from its filename.
DataFormats	This class contains the definition of some DataFormats.
DataList	This class define a data list.
DataMetadata	This interface define metadata of data objects.
DataMetadataStorage	This class define a storage for data metadata of all files generated by the workflow.
DataProtocol	This interface define a protocol.
DataProtocolService	This class define a service to retrieve a DataProtocol.
DataToolElement	The Class ToolOutputsData.
DataUtils	This class define an utility on data object.
DeepToolsModule	This class uses tools from the DeepTools suite.
DefaultDesignReader	This class allow to read a design file whatever the underlying design format.
DefaultExecutorInterpreter	This class define the default executor interpreter.
DefineDataFormatToDownload	This Step allow to define the list of the formats of the files to download at the end of a Hadoop execution.
DeprecatedDataProtocol	This class define a deprecated protocol.
DESeq2DesignChecker	This class define a Checker on the design for DESeq2 analyzes.
DESeq2Module	Class to run the differential analysis with DEseq2
DESeq2Parameters	This class contains DESeq2 module parameters.
DESeq2Parameters.FitType	Enum for the fitType option in DESeq2 related to the dispersion estimation.
DESeq2Parameters.SizeFactorsType	Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.
DESeq2Parameters.StatisticTest	Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysis
Design	This interface defines the design.
DesignBuilder	This class allow to easily build Design object from files paths.
DesignFactory	This class is a factory for experimental design.
DesignFormatFinderInputStream	This class allow to automatically detect the format of a design file.
DesignMetadata	This interface defines the design metadata.
DesignMetadataImpl	This class defines the default implementation of the design metadata.
DesignModule	This class define a design module.
DesignReader	This interface define a DesignReader.
DesignUtils	Utils methods for Design.
DesignWriter	This interface define a writer for designs.
DiffAna	This class create and launch a R script to compute differential analysis.
DiffAna.DispersionFitType	Dispersion estimation fitType enum for DESeq differential analysis
DiffAna.DispersionMethod	Dispersion estimation method enum for DESeq differential analysis
DiffAna.DispersionSharingMode	Dispersion estimation sharingMode enum for DESeq differential analysis
DiffAnaModule	This class define the module of differential analysis in local mode.
DiffanaResultsAnnotationModule	This class define a module that create annotated expression files in TSV, ODS or XLSX format.
DistCp	A Map-reduce program to recursively copy directories between different file-systems.
DistCp.DuplicationException	An exception class for duplicated source files.
DistributedLock	Distributed locking via ZooKeeper.
DistributedLocker	This class implements a locker using Zookeeper based on Twiter's DistributedLock class.
DockerExecutorInterpreter	This class define a Docker executor interpreter.
DockerRequirement	This class define a Docker requirement.
DockerRExecutor	This class define a Docker RExecutor.
DummyGeneratorModule	This class implements a dummy generator module that create an empty file.
DummyTaskScheduler	This class define a Dummy cluster scheduler.
EasyContrasts1	This class allow to execute easy contrasts 1.
EasyContrasts2	This class allow to execute easy contrasts 2.
EmergencyStopTask	This interface define a task that will executed if the execution of the workflow fail.
EmergencyStopTasks	This class define a class where the emergency tasks are stored
EmptyFileQC	Empty file FastQC module.
EmptyToolElement	This class define an empty tool element.
Eoulsan1DesignReader	This class define a design reader for limma design files.
Eoulsan1DesignWriter	This class implements a writer for limma design files.
Eoulsan2DesignReader	This class define a design reader for Eoulsan 2 design file.
Eoulsan2DesignWriter	This class implements a writer for Eoulsan 2 design files.
EoulsanAnnotationUtils	This class contains annotation utilities.
EoulsanDockerManager	This class define a Docker manager configurated with Eoulsan settings.
EoulsanError	A nestable Eoulsan error.
EoulsanException	A nestable Eoulsan exception.
EoulsanITRuntimeException	This class define a runtime exception for integration tests.
EoulsanLogger	This class allow to change the logger name for all Eoulsan classes.
EoulsanRuntime	This class store the only Eoulsan runtime instance.
EoulsanRuntimeException	A nestable Eoulsan exception.
EoulsanTranslatorUtils	This class define Kenetre translator utility glue methods for Eoulsan.
EoulsanUtils	Utility methods that will be soon merged in Kenetre.
ExecAction	This class define the Local exec Action.
ExecFileLock	This class define a lock file.
ExecJarHadoopAction	This class define an action that allow to execute a jar on an Hadoop cluster.
ExecLock	This class define a lock to prevent execution of a process simultaneously on multiples JVM.
ExecutionMode	This class define an enum for the execution mode of Eoulsan.
Executor	This class is the executor for running all the steps of an analysis.
ExecutorArguments	This class contains arguments for the Executor.
ExecutorInterpreter	This interface define a executor interpreter for Galaxy tools.
Experiment	This interface defines an experiment.
ExperimentImpl	This class defines the default implementation of an experiment.
ExperimentMetadata	This interface defines the experiment metadata.
ExperimentSample	This interface defines the experiment sample.
ExperimentSampleImpl	This class defines the default implementation of the experiment sample.
ExperimentSampleMetadata	This inteface defines the experiment sample metadata.
ExperimentSampleMetadataImpl	This class defines the default implementation of the experiment sample metadata.
ExpressionCounterCounter	This enum define counters for the expression step.
ExpressionCounterUtils	This class define some glue methods between Eoulsan and Kenetre.
ExpressionHadoopModule	This class is the main class for the expression program of the reads in hadoop mode.
ExpressionInputPreprocessor	This class define a preprocessor for expression reports.
ExpressionLocalModule	This class is the module to compute expression in local mode
ExpressionMapper	Mapper for the expression estimation.
ExpressionMerger	This class define a merger class for expression files.
ExpressionOutputFormat	This class define a expression output format.
ExpressionRecordWriter	This class define a RecordWriter for expression files.
ExpressionReducer	Reducer for the expression estimation.
ExpressionResultsAnnotationModule	This class define a module that create annotated expression files in TSV, ODS or XLSX format.
ExpressionSAMOutputMapper	Mapper for the expression estimation with a SAM output.
ExpressionSplitter	This class define a splitter class for expression files.
ExpressionToMatrixModule	This class define a class that allow to merge expression file into a matrix file.
FailModule	This module is a module that always fails.
FakeModule	This module is a fake module.
FastQCFixInputPreprocessor	This class define a preprocessor for FastQC reports.
FastQCInputPreprocessor	This class define a preprocessor for FastQC reports.
FastQCModule	This class define a module that compute QC report using FastQC.
FastQCRuntimePatcher	This class to patch FastQC to be compatible with Hadoop.
FastqInputFormat	This class define an InputFormat for FASTQ files for the Hadoop MapReduce framework.
FastqLineRecordReader	Treats keys as offset in file and value as line.
FastqMerger	This class define a merger class for FASTQ files.
FastqOutputFormat	This class define a FASTQ output format.
FastqRecordReader	This class define a RecordReader for FASTQ files for the Hadoop MapReduce framework.
FastqRecordWriter	This class define a RecordWriter for FASTQ files.
FastqSequenceFile	This class define a SequenceFile for FASTQ files.
FastqSplitter	This class define a splitter class for FASTQ files.
FeatureCountsInputPreprocessor	This class define a preprocessor for FeatureCounts reports.
FileCharsets	This class define default charsets.
FileConcatInputStream	This class define an InputStream that concatenate files in an InputStream.
FileDataProtocol	This class implements a File Protocol.
FileNaming	This class contains methods to create workflow data file names.
FileNamingParsingRuntimeException	This class define a runtime exception for filename parsing errors.
FileResourceLoader<S>	This class allow to define a resource loader for files.
FilterAndMapReadsHadoopModule	This class define a Step that filter and map read in Hadoop mode.
FinalExpressionFeaturesCreator	This class generates the final expression file after counting the alignments for each feature with HTSeq-count.
FirstModule	This class define a first module that do nothing.
FloatParameterToolElement	This class define a float tool element parameter.
FormatsAction	This class define an action that show the list of available formats.
FTPPathDataProtocol	This class define the FTP protocol in Hadoop mode.
FTPURLDataProtocol	This class define the ftp protocol in local mode.
GalaxyToolInterpreter	This class create an interpreter to tool xml file from Galaxy.
GalaxyToolModule	The Class GalaxyToolStep.
GalaxyToolXMLParserUtils	This class define static utils methods to extract data in Galaxy tool XML file.
Generator	This annotation is used to mark a step class that is a generator with user custom parameters.
GenericExecutorInterpreter	This class define a generic executor interpreter.
GenericStorageGeneratorModule	This module allow to easily store output of generator to avoid computation at each Eoulsan startup.
GenomeChecker	This class define a Checker on genome FASTA files.
GenomeDataProtocol	This class define a genome protocol.
GenomeDescriptionCreator	This class define a genome description creator.
GenomeDescriptionGeneratorModule	This class implements a genome description generator module.
GenomeMapperIndexGeneratorModule	This class define a module that generate a genome mapper index.
GFFChecker	This class define a Checker on GFF annotation.
GFFDataProtocol	This class define a annotation protocol.
GFFFastaGeneratorModule	This generator allow to generate a genome fasta file from the fasta section of a GFF file.
Globals	This class contains globals constants for the application.
GTFChecker	This class define a Checker on GTF annotation.
GTFDataProtocol	This class define a annotation protocol.
HadoopBamUtils
HadoopCompatible	This annotation is used to mark a plug-in class as usable in hadoop mode and local mode.
HadoopCompatibleTaskScheduler	This class is a scheduler for tasks from step with the @HadoopComptible annotation in Hadoop mode.
HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
HadoopCompressionCodecs	This class allow to create input and output stream for compression codec of Hadoop.
HadoopEoulsanRuntime	This class define the Runtime to execute low level IO operation for Eoulsan in Hadoop mode.
HadoopExecAction	This class launch Eoulsan in hadoop mode.
HadoopInfo	This class show in log some Hadoop information.
HadoopJarRepackager	This class allow to repackage the application.
HadoopJobEmergencyStopTask	This class define an EmergencyStopTask for Hadoop Jobs.
HadoopMappingUtils	This class contains utility methods for the Hadoop mapping package classes.
HadoopOnly	This annotation is used to mark a plug-in class as usable in hadoop mode only.
HadoopReporter	This class define a Hadoop reporter.
HadoopReporterIncrementer	This class define a Hadoop reporter.
HadoopUploadModule	This class define a module for Hadoop file uploading.
HDFSDataDownloadModule	This class define a download module that retrieve data from HDFS at the end of an analysis.
HDFSPathDataProtocol	This class define the HDFS protocol in Hadoop mode.
HTCondorTaskScheduler	This class define a HTCondor cluster scheduler using a Bpipe script.
HTMLReportArchiveNeigborClass	Empty class for patching the HTMLReportArchive class of FastQC.
HTTPPathDataProtocol	This class define the HTTP protocol in Hadoop mode.
HTTPSPathDataProtocol	This class define the HTTP protocol in Hadoop mode.
HTTPSURLDataProtocol	This class define the http protocol in local mode.
HTTPURLDataProtocol	This class define the http protocol in local mode.
IDRModule	This class defines the IDR quality check step.
ImportModule	This class define a import step.
InfoAction	This class define an action that show the Eoulsan configuration
Infos	This class gathers information about Eoulsan configuration and system environment.
Infos.Info	This class define an info.
InputPort	This interface define an input port of a step.
InputPorts	This interface define a group of input ports.
InputPortsBuilder	This class allow to easily create input ports for a step.
InputPreprocessor	This interface define a preprocessor for MultiQC input data.
InputPreprocessorService	This class define a service to retrieve a InputPreprocessor.
IntegerParameterToolElement	This class define an integer tool element parameter.
IntegrationTestAction	This class launch integration test with Testng class.
JarRepack	This class allow to repackage a jar file.
LanternaUI	This class define an UI using Lanterna library.
LinuxCpuInfo	Get information about processor on Linux systems.
LinuxInfo	This class define a linux info file parser.
LinuxMemInfo	Get information about memory on Linux systems
LocalEoulsanRuntime	This class define the Runtime to execute low level IO operation for Eoulsan in local mode.
LocalOnly	This annotation is used to mark a plug-in class as usable in local mode only.
LocalUploadModule	This class define a Step for local mode file uploading.
Locker	This interface define an interface for the global execution locker.
LockerUtils	Utility class for the locker classes.
MACS2Module	This class defines the macs2 peak-calling step.
Main	This class is the main class.
MainCLI	Main class in local mode.
MainHadoop	Main class in Hadoop mode.
MapperIndexDataFormat	This class define a DataFormat from an XML file.
MapperInputPreprocessor	This class define a preprocessor for mapper reports.
MappingCounters	This enum define the names of the counters of the steps of this package.
MapReduceUtils	This class contains utility method to easily manipulate the new Hadoop MapReduce API.
MatrixToCellRangerMatrixModule	This class define a class that allow to create a Cell Ranger matrix from an existing matrix file.
MaxByteInputStream	This class allow to create an InputStream that can read a maximum of byte from another InputStream.
MergeInputRepLocalModule	This class merges SAM files of input of the same experiment.
MergePeaksModule	This class defines the peak merging step.
Merger	This interface define a splitter.
MergerModule	This class define a generic merger module.
Metadata	This interface defines common methods for metadata.
Minimap2IndexGeneratorModule	This class define a module that generate a Minimap2 mapper index.
Module	This interface define a Module.
ModuleRegistry	This class define a registry for modules.
Modules	This class contains useful methods for writing Step classes.
ModulesAction	This class define an action that show the list of available formats.
ModuleService	This class allow to get a Step object from a class in the classpath.
MonoThreadTaskScheduler	This class define a mono thread scheduler.
MultiQCModule	This class define a module for MultiQC.
MultiThreadTaskScheduler	This class define a muti thread scheduler.
Naming	This class contains methods to validate workflow object names.
NoLog	This annotation is used to mark a step class that requires no log.
NoOutputDirectory	This annotation is used to mark a step class that requires no output directory.
Normalization	This class create and launch an R script to compute normalisation of expression data
NormalizationModule	This class define the module for normalization
NoUI	This class define an UI that do nothing.
OtherLogConfigurator	This class allow to configure non Eoulsan log using Log4J.
OutputPort	This interface define an output port of a step.
OutputPorts	This interface define a group of output ports.
OutputPortsBuilder	This class allow to easily create input ports for a step.
PairedEndFastqToTfq	This class allow to convert two FASTQ file in one TFQ file.
PairedEndFastqToTfq.FastqPairedEndReducer	This class define the reducer required to convert FASTQ files into TFQ file.
ParallelizationMode	This enum define the parallelization modes of a step.
Parameter	This class define a parameter.
PathConcatInputStream	This class define an InputStream that concatenate path in an InputStream.
PathDataProtocol	This class define an abstract class for DataProtocols based on the Hadoop framework Path object.
PathRequirement	This class define a executable requirement.
PathUtils	This class define utility method to manipulate the Hadoop Path object.
PathUtils.PrefixPathFilter	Simple PathFilter to filter Paths with their beginning
PathUtils.SuffixPathFilter	Simple PathFilter to filter Paths with their suffix
PausableThreadPoolExecutor	This class define a Pausable thread pool executor.
PBSProTaskScheduler	This class define a PBSPro cluster scheduler using a Bpipe script.
Port	This interface define a port of a step.
Ports<E extends Port>	This interface define a group of ports.
PreTreatmentExpressionMapper	This class define a mapper for the pretreatment of paired-end data before the expression estimation step.
PreTreatmentExpressionReducer	This class define a reducer for the pretreatment of paired-end data before the expression estimation step.
PreTreatmentMapper	This class defines a mapper for the pretreatment of paired-end data before the reads filtering step.
PreTreatmentReducer	This class define a reducer for the pretreatment of paired-end data before the reads filtering step.
ProcessRExecutor	This class define a standard RExecutor using a system process.
ProcessUtils	Utility class for launching external process.
ProcessUtils.ProcessThreadErrOutput	This class allow to fetch standard error of the process, without printing
Progress	This interface allow to set the progress of a task.
ProgressCounterInputStream	This class implements a FilterInputStream that inform Hadoop of the progress of task using counters.
ProgressCounterOutputStream	This class implements an OutputStream that inform Hadoop of the progress of task using counters.
ReadsChecker	This class define a checker on FASTQ files.
ReadsFilterHadoopModule	This class is the main class for the filter reads program in hadoop mode.
ReadsFilterLocalModule	This class define a module for reads filtering.
ReadsFilterMapper	This class defines a read filter mapper.
ReadsMapperHadoopModule	This class define an mapper module in Hadoop mode.
ReadsMapperLocalModule	This class define a module for reads mapping.
ReadsMapperMapper	This class defines a generic mapper for reads mapping.
Requirement	This interface define a requirement for an Eoulsan Step.
RequirementInstallerModule	This class allow to install a requirement.
RequirementService	This class define a service for requirements.
RequiresAllPreviousSteps	This annotation is used to mark a step class that requires the all the previous step in the workflow file.
RequiresPreviousStep	This annotation is used to mark a step class that requires the previous step in the workflow file.
ResourceLoader<S>	This interface define a resource loader.
ReuseModuleInstance	This annotation is used to mark a module class that can reuse a module instance for each task.
RExecutor	This interface define how to prepare, launch and retrieve data of a R analysis.
RExecutorFactory	This class define a factory to create RExecutor objects.
RExecutorFactory.Mode	Define a enum for the mode of RExecutor.
RmDupLocalModule	This class removes PCR duplicates from a SAM file.
RModuleCommonConfiguration	This class define common methods used for the configuration of the step of the package.
RnaSeqMetricsInputPreprocessor	This class define a preprocessor for Picard RnaSeqMetrics reports.
RSConnection	This class define an enhanced connection to RServe.
RserveRequirement	This class define a Rserve server requirement.
RserveRExecutor	This class define a RServe RExecutor.
RSingleCellExperimentCreatorModule	This class define a class that allow to create a SingleCellExperiment Bioconductor Object and save it as a RDS file.
SAM2BAMHadoopModule	This class define a module for converting SAM files into BAM.
SAM2BAMLocalModule	This class define a module for converting SAM files into BAM.
SAM2FASTQLocalModule	This class define a module for converting SAM files into FASTQ.
SAMFilterHadoopModule	This class define a filter alignment step in Hadoop mode.
SAMFilterLocalModule	This class define a Step for alignments filtering.
SAMFilterMapper	This class defines a mapper for alignment filtering.
SAMFilterReducer	This class define a reducer for alignments filtering.
SAMHeaderHadoopUtils	This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.
SAMHeaderHadoopUtils.SAMHeaderWriter	This class allow to save the SAM header read by a mapper.
SAMInputFormat	This class define an InputFormat for SAM files for the Hadoop MapReduce framework.
SAMMerger	This class define a merger class for SAM files.
SAMOutputFormat	This class define a SAM output format.
Sample	This interface defines a sample.
SampleMetadata	This interface defines the sample metadata.
SAMRecordReader	This class define a RecordReader for SAM files for the Hadoop MapReduce framework.
SAMRecordWriter	This class define a RecordWriter for SAM files.
SAMSequenceFile	This class define a SequenceFile for SAM files.
SAMSplitter	This class define a splitter class for SAM files.
SelectParameterToolElement	This class define a select tool element parameter.
SerializableStopwatch
Settings	This class define a settings class.
ShellModule	This class define a module that execute a shell command.
SimpleInputPort	This class define an input port of a step.
SimpleInputPorts	This class define a class that handles a set of input ports.
SimpleOutputPort	This class define an output port of a step.
SimpleOutputPorts	This class define a class that contains several output ports.
SLURMTaskScheduler	This class define a SLURM cluster scheduler using a Bpipe script.
Splice2BEDModule	This class define a module for converting SAM files into BED.
SplitReadsModule	This class define a module for reads splitting.
Splitter	This interface define a splitter.
SplitterModule	This class define a generic splitter module.
STARIndexGeneratorModule	This class define a module that generate a STAR mapper index.
Step	This interface define a step of the workflow.
Step.DiscardOutput	This enum define the value of the discard output attribute of the step tag in the Eoulsan workflow file.
Step.StepState	This enum define the states of the steps.
Step.StepType	This enum define the type of step.
StepConfigurationContext
StepConfigurationContextImpl	This class define a concrete implementation of the configuration context of a step.
StepInstances	This class store module instances and avoid storing this instance in Step objects that are serialized.
StepObserver	This interface define workflow step events
StepObserverRegistry	This class allow to relay workflow step events to other observers.
StepOutputDataFile	This class define an output file of workflow set.
StepResult	This class define a step result.
StepStateDependencies	This class allow to store the step state and its dependencies.
StepStatus	This class define a step status.
StorageDataProtocol	This abstract class define a storage protocol.
TaskContext	This interface define the context of a step.
TaskContextImpl	This class define a task context.
TaskResult	This class define the result of a step.
TaskResultImpl	This class define a result for a task context.
TaskRunner	This class allow to run a task context.
TaskScheduler	This interface define a task scheduler.
TaskSchedulerFactory	This class define a factory for TaskScheduler that can create only one instance.
TaskSerializationUtils	This class contains utility methods for serialization, deserialization and execution of Task objects.
TaskStatus	This interface define a step status.
TaskStatusImpl	This class define a task status.
TechnicalReplicateMergerModule	This class define a merger module for technical replicates.
Terminal	This annotation is used to mark a step class that is a terminal step.
TerminalModule	This class define a terminal task that do nothing.
TextParameterToolElement	This class define a text tool element parameter.
TGCCTaskScheduler	This class define a TGCC cluster scheduler.
Ticket	This class define a ticket for the TicketLocker.
TicketLocker	This class define a global locker using RMI messaging.
TicketScheduler	Define the rmi interface for the TicketSchedulerServer.
TicketSchedulerServer	This class define a server for the scheduler.
TokenManager	This class define a token manager for a step.
TokenManagerRegistry	This class store all the TokenManager instances.
ToolElement	The ToolElement interface.
ToolElementFactory	This class define a factory for ToolElement objects.
ToolExecutor	The class define an executor on tool set in XML file.
ToolExecutorResult	The class define a result on execution tool.
ToolInfo	The class define a tool data which contains all data extracted from XML file.
TORQUETaskScheduler	This class define a TORQUE cluster scheduler using a Bpipe script.
TrackHubModule	This class construct TrackHub for genome browser visualization.
UI	This interface define how UI is informed of The workflow changes.
UIEvent	This class define an abstract UIEvent
UIService	This class define a service to retrieve a UI.
UIStepEvent	This class define a UI step event.
UITaskEvent	This class define a UI task event.
UIWorkflowEvent	This class define a UI workflow event.
UnmodifiableData	This class define an unmodifiable data
UnmodifiableExperiment
UnmodifiableExperimentMetadata
UnmodifiableExperimentSampleMetadata
UploadModule	This class define a abstract module class for files uploading.
URLDataProtocol	This class define an abstract class for DataProtocols based on the URL class.
Utils
Workflow	This interface define a Workflow.
Workflow2Graphviz	Convert a Workflow to Graphviz
WorkflowContext	This class define the context implementation.
WorkflowDataUtils	This class define an utility on data object.
WorkflowEventBus	This class define a single for the event bus.
WorkflowFileNaming	This class contains methods to create workflow data file names.
XMLDataFormat	This class define a DataFormat from an XML file.
ZooKeeperLocker	This class implements a locker using Zookeeper.