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

Packages that use TaskContext

Package	Description
fr.ens.biologie.genomique.eoulsan.core	This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.workflow	This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.galaxytools	This package contain classes related to read tool xml file from galaxy.
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.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 TaskContext in fr.ens.biologie.genomique.eoulsan.core

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

Modifier and Type	Method	Description
TaskResult	Module.execute(TaskContext context, TaskStatus status)	Execute a task step.
static DataFile	ContextUtils.getHadoopWorkingDirectory(TaskContext context)	Get the Hadoop working directory.
static DataFile	ContextUtils.getJarPathname(TaskContext context)	Get the application jar file.
static DataFile	ContextUtils.getJobDirectory(TaskContext context)	Get the job directory.
static DataFile	ContextUtils.getLocalWorkingDirectory(TaskContext context)	Get the local working directory.
static DataFile	ContextUtils.getTaskOutputDirectory(TaskContext context)	Get the task output directory.

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

Classes in fr.ens.biologie.genomique.eoulsan.core.workflow that implement TaskContext

Modifier and Type	Class	Description
class	TaskContextImpl	This class define a task context.

Uses of TaskContext in fr.ens.biologie.genomique.eoulsan.galaxytools

Methods in fr.ens.biologie.genomique.eoulsan.galaxytools with parameters of type TaskContext

Modifier and Type	Method	Description
ToolExecutorResult	GalaxyToolInterpreter.execute(TaskContext context)	Convert command tag from tool file in string, variable are replace by value.

Constructors in fr.ens.biologie.genomique.eoulsan.galaxytools with parameters of type TaskContext

Constructor	Description
ToolExecutor(TaskContext context, ToolInfo toolData, String commandLine, Set<File> inputFiles)	Constructor a new galaxy tool executor.

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

Methods in fr.ens.biologie.genomique.eoulsan.modules with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	CheckerModule.execute(TaskContext context, TaskStatus status)
TaskResult	CopyInputDataModule.execute(TaskContext context, TaskStatus status)
TaskResult	CopyOutputDataModule.execute(TaskContext context, TaskStatus status)
TaskResult	DesignModule.execute(TaskContext context, TaskStatus status)
TaskResult	FailModule.execute(TaskContext context, TaskStatus status)
TaskResult	FakeModule.execute(TaskContext context, TaskStatus status)
TaskResult	FirstModule.execute(TaskContext context, TaskStatus status)
TaskResult	GalaxyToolModule.execute(TaskContext context, TaskStatus status)
TaskResult	ImportModule.execute(TaskContext context, TaskStatus status)
TaskResult	MergerModule.execute(TaskContext context, TaskStatus status)
TaskResult	RequirementInstallerModule.execute(TaskContext context, TaskStatus status)
TaskResult	ShellModule.execute(TaskContext context, TaskStatus status)
TaskResult	SplitterModule.execute(TaskContext context, TaskStatus status)
TaskResult	TerminalModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	MergeInputRepLocalModule.execute(TaskContext context, TaskStatus status)	Merge input replicates.
TaskResult	RmDupLocalModule.execute(TaskContext context, TaskStatus status)
TaskResult	TrackHubModule.execute(TaskContext context, TaskStatus status)	Run trackhub generator.

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	BedToolsModule.execute(TaskContext context, TaskStatus status)	Run bedtools multiinter.
TaskResult	DeepToolsModule.execute(TaskContext context, TaskStatus status)	Run deeptools.
TaskResult	MACS2Module.execute(TaskContext context, TaskStatus status)	Run macs2.
TaskResult	MergePeaksModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	CountSplicedReadsModule.execute(TaskContext context, TaskStatus status)	Install all the files necessary in the tmp folder, then run idr.
TaskResult	IDRModule.execute(TaskContext context, TaskStatus status)	Install all the files necessary in the tmp folder, then run idr.

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	DESeq2Module.execute(TaskContext context, TaskStatus status)
TaskResult	DiffAnaModule.execute(TaskContext context, TaskStatus status)
TaskResult	DiffanaResultsAnnotationModule.execute(TaskContext context, TaskStatus status)
TaskResult	NormalizationModule.execute(TaskContext context, TaskStatus status)
protected String	DiffAna.generateScript(Experiment experiment, TaskContext context)
protected String	Normalization.generateScript(Experiment experiment, TaskContext context)	Generate the R script.
void	Normalization.run(TaskContext context, Data data)	Run normalisation step
protected void	Normalization.runRExecutor(TaskContext context, Data data)	Execute Rnw script.

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	ExpressionResultsAnnotationModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	ExpressionHadoopModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.local with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	ExpressionLocalModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.fastqc with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	FastQCModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.generators with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	DummyGeneratorModule.execute(TaskContext context, TaskStatus status)
TaskResult	GenericStorageGeneratorModule.execute(TaskContext context, TaskStatus status)
TaskResult	GenomeDescriptionGeneratorModule.execute(TaskContext context, TaskStatus status)
TaskResult	GenomeMapperIndexGeneratorModule.execute(TaskContext context, TaskStatus status)
TaskResult	GFFFastaGeneratorModule.execute(TaskContext context, TaskStatus status)
TaskResult	Minimap2IndexGeneratorModule.execute(TaskContext context, TaskStatus status)
TaskResult	STARIndexGeneratorModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	FilterAndMapReadsHadoopModule.execute(TaskContext context, TaskStatus status)
TaskResult	ReadsFilterHadoopModule.execute(TaskContext context, TaskStatus status)
TaskResult	ReadsMapperHadoopModule.execute(TaskContext context, TaskStatus status)
TaskResult	SAM2BAMHadoopModule.execute(TaskContext context, TaskStatus status)
TaskResult	SAMFilterHadoopModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.local with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	BAM2SAMLocalModule.execute(TaskContext context, TaskStatus status)
TaskResult	ReadsFilterLocalModule.execute(TaskContext context, TaskStatus status)
TaskResult	ReadsMapperLocalModule.execute(TaskContext context, TaskStatus status)
TaskResult	SAM2BAMLocalModule.execute(TaskContext context, TaskStatus status)
TaskResult	SAM2FASTQLocalModule.execute(TaskContext context, TaskStatus status)
TaskResult	SAMFilterLocalModule.execute(TaskContext context, TaskStatus status)
TaskResult	Splice2BEDModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	CopyDesignAndWorkflowFilesToOutputModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	DefineDataFormatToDownload.execute(TaskContext context, TaskStatus status)
TaskResult	HDFSDataDownloadModule.execute(TaskContext context, TaskStatus status)
TaskResult	UploadModule.execute(TaskContext context, TaskStatus status)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	MultiQCModule.execute(TaskContext context, TaskStatus status)
void	ExpressionInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)
void	FastQCInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)
void	FeatureCountsInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)
void	InputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)	Preprocess data.
void	MapperInputPreprocessor.preprocess(TaskContext context, Data data, File multiQCInputDirectory)

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

Methods in fr.ens.biologie.genomique.eoulsan.modules.singlecell with parameters of type TaskContext

Modifier and Type	Method	Description
TaskResult	ExpressionToMatrixModule.execute(TaskContext context, TaskStatus status)
TaskResult	MatrixToCellRangerMatrixModule.execute(TaskContext context, TaskStatus status)
TaskResult	RSingleCellExperimentCreatorModule.execute(TaskContext context, TaskStatus status)