Uses of Interface
fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
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Packages that use StepConfigurationContext 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.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.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 StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.core
Subinterfaces of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.core Modifier and Type Interface Description interface
TaskContext
This interface define the context of a step.Methods in fr.ens.biologie.genomique.eoulsan.core with parameters of type StepConfigurationContext Modifier and Type Method Description static void
Modules. badParameterValue(StepConfigurationContext context, Parameter parameter, String message)
Throw a exception for bad parameter value.void
Module. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the module.static void
Modules. deprecatedParameter(StepConfigurationContext context, Parameter parameter)
Show a message for deprecated parameters.static void
Modules. deprecatedParameter(StepConfigurationContext context, Parameter parameter, boolean throwException)
Show a message for deprecated parameters.static void
Modules. invalidConfiguration(StepConfigurationContext context, String message)
Throw a exception for an invalid configuration.static void
Modules. removedParameter(StepConfigurationContext context, Parameter parameter)
Throw a exception for removed parameters.static void
Modules. renamedParameter(StepConfigurationContext context, Parameter parameter, String newParameterName)
Show a message for deprecated parameters that has been renamed.static void
Modules. renamedParameter(StepConfigurationContext context, Parameter parameter, String newParameterName, boolean throwException)
Show a message for deprecated parameters that has been renamed.static void
Modules. unknownParameter(StepConfigurationContext context, Parameter parameter)
Throw a exception for unknown parameters. -
Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.core.workflow
Classes in fr.ens.biologie.genomique.eoulsan.core.workflow that implement StepConfigurationContext Modifier and Type Class Description class
StepConfigurationContextImpl
This class define a concrete implementation of the configuration context of a step.class
TaskContextImpl
This class define a task context. -
Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules
Methods in fr.ens.biologie.genomique.eoulsan.modules with parameters of type StepConfigurationContext Modifier and Type Method Description void
AbstractModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
CopyInputDataModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
CopyOutputDataModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
DesignModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
FailModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
FakeModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
GalaxyToolModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
ImportModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
MergerModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
RequirementInstallerModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
ShellModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
SplitterModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.chipseq
Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq with parameters of type StepConfigurationContext Modifier and Type Method Description void
MergeInputRepLocalModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step.void
RmDupLocalModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step.void
TrackHubModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step. -
Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling with parameters of type StepConfigurationContext Modifier and Type Method Description void
BedToolsModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step.void
DeepToolsModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step.void
MACS2Module. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step.void
MergePeaksModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step. -
Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc
Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc with parameters of type StepConfigurationContext Modifier and Type Method Description void
CountSplicedReadsModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step.void
IDRModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set IDR parameters to configure the step. -
Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.diffana
Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type StepConfigurationContext Modifier and Type Method Description void
DESeq2Module. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
DiffAnaModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
DiffanaResultsAnnotationModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
NormalizationModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
static RExecutor
RModuleCommonConfiguration. parseRExecutorParameter(StepConfigurationContext context, Set<Parameter> stepParameters, Set<Requirement> requirements, String defaultDockerImage)
Parse the step parameter and create a configured RExecutor object. -
Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.expression
Methods in fr.ens.biologie.genomique.eoulsan.modules.expression with parameters of type StepConfigurationContext Modifier and Type Method Description void
AbstractExpressionModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
ExpressionResultsAnnotationModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop with parameters of type StepConfigurationContext Modifier and Type Method Description void
ExpressionHadoopModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.fastqc
Methods in fr.ens.biologie.genomique.eoulsan.modules.fastqc with parameters of type StepConfigurationContext Modifier and Type Method Description void
FastQCModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.generators
Methods in fr.ens.biologie.genomique.eoulsan.modules.generators with parameters of type StepConfigurationContext Modifier and Type Method Description void
GenericStorageGeneratorModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
GenomeMapperIndexGeneratorModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
Minimap2IndexGeneratorModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
STARIndexGeneratorModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mapping
Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping with parameters of type StepConfigurationContext Modifier and Type Method Description void
AbstractBAM2SAMModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
AbstractFilterAndMapReadsModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
AbstractReadsFilterModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
AbstractReadsMapperModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
AbstractSAM2BAMModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
AbstractSAM2FASTQModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
AbstractSAMFilterModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
AbstractSplice2BEDModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop with parameters of type StepConfigurationContext Modifier and Type Method Description void
FilterAndMapReadsHadoopModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
ReadsMapperHadoopModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop
Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop with parameters of type StepConfigurationContext Modifier and Type Method Description void
CopyDesignAndWorkflowFilesToOutputModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type StepConfigurationContext Modifier and Type Method Description void
DefineDataFormatToDownload. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
HDFSDataDownloadModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.multiqc
Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc with parameters of type StepConfigurationContext Modifier and Type Method Description void
MultiQCModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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Uses of StepConfigurationContext in fr.ens.biologie.genomique.eoulsan.modules.singlecell
Methods in fr.ens.biologie.genomique.eoulsan.modules.singlecell with parameters of type StepConfigurationContext Modifier and Type Method Description void
ExpressionToMatrixModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
MatrixToCellRangerMatrixModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void
RSingleCellExperimentCreatorModule. configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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