Class CommandStep
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
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- fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep
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- All Implemented Interfaces:
Step
,Serializable
public class CommandStep extends AbstractStep
This class define a step based on a Command object (workflow file).- Since:
- 2.0
- Author:
- Laurent Jourdren
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface fr.ens.biologie.genomique.eoulsan.core.Step
Step.DiscardOutput, Step.StepState, Step.StepType
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Constructor Summary
Constructors 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.CommandStep(AbstractWorkflow workflow, Step.StepType type)
Constructor that create a step with nothing to execute like ROOT_STEP, DESIGN_STEP and FIRST_STEP.CommandStep(AbstractWorkflow workflow, DataFormat format)
Create a Generator Workflow step.CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct)
Create a step for a standard step.CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct, DataFile outputDirectory)
Create a step for a standard step.
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Method Summary
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Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
addDependency, addDependency, configure, getChecker, getDiscardOutput, getEoulsanMode, getId, getInputPorts, getModule, getModuleName, getNumber, getOutputPorts, getParallelizationMode, getParameters, getRequiredMemory, getRequiredProcessors, getState, getStepOutputDirectory, getStepVersion, getType, getWorkflow, isSkip, isTerminalStep, registerInputAndOutputPorts
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Constructor Detail
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CommandStep
public CommandStep(AbstractWorkflow workflow, Step.StepType type)
Constructor that create a step with nothing to execute like ROOT_STEP, DESIGN_STEP and FIRST_STEP.- Parameters:
workflow
- the workflow of the steptype
- the type of the step
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CommandStep
public CommandStep(AbstractWorkflow workflow, DataFormat format) throws EoulsanException
Create a Generator Workflow step.- Parameters:
workflow
- the workflow objectformat
- DataFormat- Throws:
EoulsanException
- if an error occurs while configuring the generator
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CommandStep
public CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct) throws EoulsanException
Create a step for a standard step.- Parameters:
workflow
- workflow of the stepid
- identifier of the stepmoduleName
- module namestepVersion
- step versionparameters
- parameters of the stepskip
- true to skip execution of the stepdiscardOutput
- discard output valuerequiredMemory
- required memoryrequiredProcessors
- required processorsdataProduct
- data product- Throws:
EoulsanException
- id an error occurs while creating the step
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CommandStep
public CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct, DataFile outputDirectory) throws EoulsanException
Create a step for a standard step.- Parameters:
workflow
- workflow of the stepid
- identifier of the stepmoduleName
- module namestepVersion
- step versionparameters
- parameters of the stepskip
- true to skip execution of the stepdiscardOutput
- discard output valuerequiredMemory
- required memoryrequiredProcessors
- required processorsdataProduct
- data productoutputDirectory
- output directory- Throws:
EoulsanException
- id an error occurs while creating the step
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CommandStep
public CommandStep(AbstractWorkflow workflow, Module module) throws EoulsanException
Create a step for a standard step from an existing step object.- Parameters:
workflow
- workflow of the stepmodule
- module object- Throws:
EoulsanException
- id an error occurs while creating the step
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CommandStep
public CommandStep(AbstractWorkflow workflow, Module module, Set<Parameter> parameters) throws EoulsanException
Create a step for a standard step from an existing step object.- Parameters:
workflow
- workflow of the stepmodule
- module objectparameters
- parameters of the step- Throws:
EoulsanException
- id an error occurs while creating the step
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