Uses of Interface
fr.ens.biologie.genomique.eoulsan.core.Module

Packages that use Module

Package	Description
fr.ens.biologie.genomique.eoulsan.annotations	This package define the annotations on Eoulsan classes plug-ins.
fr.ens.biologie.genomique.eoulsan.core.workflow	This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.data	This package contains classes for data files, data types and data formats.
fr.ens.biologie.genomique.eoulsan.modules	This package define the steps for the Eoulsan workflow.
fr.ens.biologie.genomique.eoulsan.modules.chipseq	This packages contains the ChIP-Seq modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling	This packages contains the peak-calling modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc	This packages contains all the quality check modules for ChIP-Seq.
fr.ens.biologie.genomique.eoulsan.modules.diffana	This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.modules.expression	This package contain all the classes related to the expression step.
fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop	This package contain all the classes related to the expression step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.expression.local	This package contain all the classes related to the expression step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.fastqc	This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators	This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mapping.local	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop	This package contain classes related data management in Hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload	This package contain classes related to upload data to HDFS and Cloud.
fr.ens.biologie.genomique.eoulsan.modules.multiqc
fr.ens.biologie.genomique.eoulsan.modules.singlecell

Uses of Module in fr.ens.biologie.genomique.eoulsan.annotations

Methods in fr.ens.biologie.genomique.eoulsan.annotations with parameters of type Module

Modifier and Type	Method	Description
static boolean	EoulsanAnnotationUtils.isGenerator(Module module)	Test if a module contain the @Generator annotation.
static boolean	EoulsanAnnotationUtils.isNoLog(Module module)	Test if a module contain the @NoLog annotation.
static boolean	EoulsanAnnotationUtils.isNoOutputDirectory(Module module)	Test if a module contain the @NoOutputDirectory annotation.
static boolean	EoulsanAnnotationUtils.isRequiresAllPreviousSteps(Module module)	Test if a module contain the @RequiresPreviousStep annotation.
static boolean	EoulsanAnnotationUtils.isRequiresPreviousStep(Module module)	Test if a module contain the @RequiresPreviousStep annotation.
static boolean	EoulsanAnnotationUtils.isReuseStepInstance(Module module)	Test if a module contain the @ReuseStepInstance annotation.
static boolean	EoulsanAnnotationUtils.isTerminal(Module module)	Test if a step contain the @Terminal annotation.

Uses of Module in fr.ens.biologie.genomique.eoulsan.core.workflow

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return Module

Modifier and Type	Method	Description
Module	AbstractStep.getModule()	Get the underlying Module object.
Module	StepInstances.getModule(Step step)	Get a module instance.
Module	StepInstances.getModule(Step step, String moduleName, String moduleVersion)	Get a step instance.
Module	ModuleRegistry.loadModule(String moduleName, String version)	Load a module.

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return types with arguments of type Module

Modifier and Type	Method	Description
List<Module>	ModuleRegistry.getAllModules()	Get all the modules.

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type Module

Modifier and Type	Method	Description
protected void	AbstractStep.registerInputAndOutputPorts(Module module)
void	StepInstances.registerStep(Step step, Module module)	Register a step instance.

Method parameters in fr.ens.biologie.genomique.eoulsan.core.workflow with type arguments of type Module

Modifier and Type	Method	Description
void	Executor.execute(List<Module> firstSteps, List<Module> lastSteps)	run Eoulsan.

Constructors in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type Module

Constructor	Description
CommandStep(AbstractWorkflow workflow, Module module)	Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow workflow, Module module, Set<Parameter> parameters)	Create a step for a standard step from an existing step object.

Constructor parameters in fr.ens.biologie.genomique.eoulsan.core.workflow with type arguments of type Module

Constructor	Description
CommandWorkflow(ExecutorArguments executionArguments, CommandWorkflowModel workflowCommand, List<Module> firstSteps, List<Module> endSteps, Design design)	Public constructor.

Uses of Module in fr.ens.biologie.genomique.eoulsan.data

Methods in fr.ens.biologie.genomique.eoulsan.data that return Module

Modifier and Type	Method	Description
Module	DataFormat.getGenerator()	Get the step needed to generate the DataType from DataTypes provided by the Design file.
Module	MapperIndexDataFormat.getGenerator()
Module	XMLDataFormat.getGenerator()

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules

Classes in fr.ens.biologie.genomique.eoulsan.modules that implement Module

Modifier and Type	Class	Description
class	AbstractModule	This class define an abstract Module.
class	CheckerModule	This class is a module that launch checkers.
class	CopyInputDataModule	Copy input files of a format in another location or in different compression format.
class	CopyOutputDataModule	Copy output files of a step with a specified format to the output directory.
class	DesignModule	This class define a design module.
class	FailModule	This module is a module that always fails.
class	FakeModule	This module is a fake module.
class	FirstModule	This class define a first module that do nothing.
class	GalaxyToolModule	The Class GalaxyToolStep.
class	ImportModule	This class define a import step.
class	MergerModule	This class define a generic merger module.
class	RequirementInstallerModule	This class allow to install a requirement.
class	ShellModule	This class define a module that execute a shell command.
class	SplitterModule	This class define a generic splitter module.
class	TechnicalReplicateMergerModule	This class define a merger module for technical replicates.
class	TerminalModule	This class define a terminal task that do nothing.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.chipseq

Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq that implement Module

Modifier and Type	Class	Description
class	MergeInputRepLocalModule	This class merges SAM files of input of the same experiment.
class	RmDupLocalModule	This class removes PCR duplicates from a SAM file.
class	TrackHubModule	This class construct TrackHub for genome browser visualization.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling

Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling that implement Module

Modifier and Type	Class	Description
class	BedToolsModule	This class uses tools from the BEDTools suite.
class	DeepToolsModule	This class uses tools from the DeepTools suite.
class	MACS2Module	This class defines the macs2 peak-calling step.
class	MergePeaksModule	This class defines the peak merging step.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc

Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc that implement Module

Modifier and Type	Class	Description
class	CountSplicedReadsModule	This step computes how many spliced alignments there are in a SAM file.
class	IDRModule	This class defines the IDR quality check step.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.diffana

Classes in fr.ens.biologie.genomique.eoulsan.modules.diffana that implement Module

Modifier and Type	Class	Description
class	DESeq2Module	Class to run the differential analysis with DEseq2
class	DiffAnaModule	This class define the module of differential analysis in local mode.
class	DiffanaResultsAnnotationModule	This class define a module that create annotated expression files in TSV, ODS or XLSX format.
class	NormalizationModule	This class define the module for normalization

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.expression

Classes in fr.ens.biologie.genomique.eoulsan.modules.expression that implement Module

Modifier and Type	Class	Description
class	AbstractExpressionModule	This abstract class define and parse arguments for the expression module.
class	ExpressionResultsAnnotationModule	This class define a module that create annotated expression files in TSV, ODS or XLSX format.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop

Classes in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop that implement Module

Modifier and Type	Class	Description
class	ExpressionHadoopModule	This class is the main class for the expression program of the reads in hadoop mode.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.expression.local

Classes in fr.ens.biologie.genomique.eoulsan.modules.expression.local that implement Module

Modifier and Type	Class	Description
class	ExpressionLocalModule	This class is the module to compute expression in local mode

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.fastqc

Classes in fr.ens.biologie.genomique.eoulsan.modules.fastqc that implement Module

Modifier and Type	Class	Description
class	FastQCModule	This class define a module that compute QC report using FastQC.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.generators

Classes in fr.ens.biologie.genomique.eoulsan.modules.generators that implement Module

Modifier and Type	Class	Description
class	DummyGeneratorModule	This class implements a dummy generator module that create an empty file.
class	GenericStorageGeneratorModule	This module allow to easily store output of generator to avoid computation at each Eoulsan startup.
class	GenomeDescriptionGeneratorModule	This class implements a genome description generator module.
class	GenomeMapperIndexGeneratorModule	This class define a module that generate a genome mapper index.
class	GFFFastaGeneratorModule	This generator allow to generate a genome fasta file from the fasta section of a GFF file.
class	Minimap2IndexGeneratorModule	This class define a module that generate a Minimap2 mapper index.
class	STARIndexGeneratorModule	This class define a module that generate a STAR mapper index.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.mapping

Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping that implement Module

Modifier and Type	Class	Description
class	AbstractBAM2SAMModule	This class define a module for converting BAM files into SAM.
class	AbstractFilterAndMapReadsModule	This class define an abstract module for read filtering, mapping and alignments filtering.
class	AbstractReadsFilterModule	This class define an abstract module for read filtering.
class	AbstractReadsMapperModule	This class define an abstract module for read mapping.
class	AbstractSAM2BAMModule	This class define a module for converting SAM files into BAM.
class	AbstractSAM2FASTQModule	This class define a module for converting SAM files into BAM.
class	AbstractSAMFilterModule	This class define an abstract module for alignments filtering.
class	AbstractSplice2BEDModule	This class define a module for converting SAM files into BED.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop that implement Module

Modifier and Type	Class	Description
class	FilterAndMapReadsHadoopModule	This class define a Step that filter and map read in Hadoop mode.
class	ReadsFilterHadoopModule	This class is the main class for the filter reads program in hadoop mode.
class	ReadsMapperHadoopModule	This class define an mapper module in Hadoop mode.
class	SAM2BAMHadoopModule	This class define a module for converting SAM files into BAM.
class	SAMFilterHadoopModule	This class define a filter alignment step in Hadoop mode.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.mapping.local

Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping.local that implement Module

Modifier and Type	Class	Description
class	BAM2SAMLocalModule	This class define a module for converting BAM files into SAM.
class	ReadsFilterLocalModule	This class define a module for reads filtering.
class	ReadsMapperLocalModule	This class define a module for reads mapping.
class	SAM2BAMLocalModule	This class define a module for converting SAM files into BAM.
class	SAM2FASTQLocalModule	This class define a module for converting SAM files into FASTQ.
class	SAMFilterLocalModule	This class define a Step for alignments filtering.
class	Splice2BEDModule	This class define a module for converting SAM files into BED.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop

Classes in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop that implement Module

Modifier and Type	Class	Description
class	CopyDesignAndWorkflowFilesToOutputModule	This module copy design and workflow file to output directory.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload

Classes in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload that implement Module

Modifier and Type	Class	Description
class	DefineDataFormatToDownload	This Step allow to define the list of the formats of the files to download at the end of a Hadoop execution.
class	HadoopUploadModule	This class define a module for Hadoop file uploading.
class	HDFSDataDownloadModule	This class define a download module that retrieve data from HDFS at the end of an analysis.
class	LocalUploadModule	This class define a Step for local mode file uploading.
class	UploadModule	This class define a abstract module class for files uploading.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.multiqc

Classes in fr.ens.biologie.genomique.eoulsan.modules.multiqc that implement Module

Modifier and Type	Class	Description
class	MultiQCModule	This class define a module for MultiQC.

Uses of Module in fr.ens.biologie.genomique.eoulsan.modules.singlecell

Classes in fr.ens.biologie.genomique.eoulsan.modules.singlecell that implement Module

Modifier and Type	Class	Description
class	ExpressionToMatrixModule	This class define a class that allow to merge expression file into a matrix file.
class	MatrixToCellRangerMatrixModule	This class define a class that allow to create a Cell Ranger matrix from an existing matrix file.
class	RSingleCellExperimentCreatorModule	This class define a class that allow to create a SingleCellExperiment Bioconductor Object and save it as a RDS file.