Uses of Interface
fr.ens.biologie.genomique.eoulsan.core.TaskResult
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Packages that use TaskResult 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.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 -
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.core
Methods in fr.ens.biologie.genomique.eoulsan.core that return TaskResult Modifier and Type Method Description TaskResult
TaskStatus. createTaskResult()
Create a TaskResult object for a successful result.TaskResult
TaskStatus. createTaskResult(boolean success)
Create a TaskResult object.TaskResult
TaskStatus. createTaskResult(Throwable exception)
Create a TaskResult object.TaskResult
TaskStatus. createTaskResult(Throwable exception, String exceptionMessage)
Create a TaskResult object.TaskResult
Module. execute(TaskContext context, TaskStatus status)
Execute a task step. -
Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.core.workflow
Classes in fr.ens.biologie.genomique.eoulsan.core.workflow that implement TaskResult Modifier and Type Class Description class
TaskResultImpl
This class define a result for a task context.Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return TaskResult Modifier and Type Method Description TaskResult
TaskStatusImpl. createTaskResult()
TaskResult
TaskStatusImpl. createTaskResult(boolean success)
TaskResult
TaskStatusImpl. createTaskResult(Throwable exception)
TaskResult
TaskStatusImpl. createTaskResult(Throwable exception, String exceptionMessage)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules
Methods in fr.ens.biologie.genomique.eoulsan.modules that return TaskResult 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)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.chipseq
Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq that return TaskResult 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 TaskResult in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling that return TaskResult 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)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc
Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc that return TaskResult 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 TaskResult in fr.ens.biologie.genomique.eoulsan.modules.diffana
Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana that return TaskResult 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)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.expression
Methods in fr.ens.biologie.genomique.eoulsan.modules.expression that return TaskResult Modifier and Type Method Description TaskResult
ExpressionResultsAnnotationModule. execute(TaskContext context, TaskStatus status)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop that return TaskResult Modifier and Type Method Description TaskResult
ExpressionHadoopModule. execute(TaskContext context, TaskStatus status)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.expression.local
Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.local that return TaskResult Modifier and Type Method Description TaskResult
ExpressionLocalModule. execute(TaskContext context, TaskStatus status)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.fastqc
Methods in fr.ens.biologie.genomique.eoulsan.modules.fastqc that return TaskResult Modifier and Type Method Description TaskResult
FastQCModule. execute(TaskContext context, TaskStatus status)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.generators
Methods in fr.ens.biologie.genomique.eoulsan.modules.generators that return TaskResult 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)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop that return TaskResult 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)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.local that return TaskResult 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)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop
Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop that return TaskResult Modifier and Type Method Description TaskResult
CopyDesignAndWorkflowFilesToOutputModule. execute(TaskContext context, TaskStatus status)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload that return TaskResult 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)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.multiqc
Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc that return TaskResult Modifier and Type Method Description TaskResult
MultiQCModule. execute(TaskContext context, TaskStatus status)
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Uses of TaskResult in fr.ens.biologie.genomique.eoulsan.modules.singlecell
Methods in fr.ens.biologie.genomique.eoulsan.modules.singlecell that return TaskResult 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)
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