Uses of Annotation Interface
fr.ens.biologie.genomique.eoulsan.annotations.LocalOnly

Packages that use LocalOnly

Package	Description
fr.ens.biologie.genomique.eoulsan.data.protocols	This package contains class for protocols used by the DataFile classes.
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.local	This package contain all the classes related to the expression step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.generators	This package contain generator steps.
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.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 LocalOnly in fr.ens.biologie.genomique.eoulsan.data.protocols

Classes in fr.ens.biologie.genomique.eoulsan.data.protocols with annotations of type LocalOnly

Modifier and Type	Class	Description
class	FTPURLDataProtocol	This class define the ftp protocol in local mode.
class	HTTPSURLDataProtocol	This class define the http protocol in local mode.
class	HTTPURLDataProtocol	This class define the http protocol in local mode.

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

Classes in fr.ens.biologie.genomique.eoulsan.modules with annotations of type LocalOnly

Modifier and Type	Class	Description
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	FailModule	This module is a module that always fails.
class	FakeModule	This module is a fake module.
final 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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.chipseq

Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq with annotations of type LocalOnly

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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling

Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling with annotations of type LocalOnly

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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc

Classes in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc with annotations of type LocalOnly

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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.diffana

Classes in fr.ens.biologie.genomique.eoulsan.modules.diffana with annotations of type LocalOnly

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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.expression.local

Classes in fr.ens.biologie.genomique.eoulsan.modules.expression.local with annotations of type LocalOnly

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

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

Classes in fr.ens.biologie.genomique.eoulsan.modules.generators with annotations of type LocalOnly

Modifier and Type	Class	Description
class	GenericStorageGeneratorModule	This module allow to easily store output of generator to avoid computation at each Eoulsan startup.
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 LocalOnly in fr.ens.biologie.genomique.eoulsan.modules.mapping.local

Classes in fr.ens.biologie.genomique.eoulsan.modules.mapping.local with annotations of type LocalOnly

Modifier and Type	Class	Description
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.

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

Classes in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with annotations of type LocalOnly

Modifier and Type	Class	Description
class	LocalUploadModule	This class define a Step for local mode file uploading.

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

Classes in fr.ens.biologie.genomique.eoulsan.modules.multiqc with annotations of type LocalOnly

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

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

Classes in fr.ens.biologie.genomique.eoulsan.modules.singlecell with annotations of type LocalOnly

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.