Package fr.ens.biologie.genomique.eoulsan.core.workflow

Class CommandWorkflow

java.lang.Object

fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow

fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow

All Implemented Interfaces:

Workflow, Serializable

public class CommandWorkflow
extends AbstractWorkflow

This class define a workflow based on a Command object (workflow file).

Since:

2.0

Author:

Laurent Jourdren

See Also:

Serialized Form

Field Summary

Fields inherited from class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow

WORKFLOW_COPY_FILENAME

Constructor Summary

Constructors

Constructor	Description
CommandWorkflow(ExecutorArguments executionArguments, CommandWorkflowModel workflowCommand, List<Module> firstSteps, List<Module> endSteps, Design design)	Public constructor.

Method Summary

Modifier and Type	Method	Description
protected void	saveConfigurationFiles()	Save configuration files.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow

checkDirectories, createEoulsanDataDirectoryIfRequired, createShutdownHookThread, deleteOnExit, execute, getCheckerStep, getDesign, getDesignStep, getFirstStep, getRootStep, getSteps, getWorkflowContext, register, stepStateEvent

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CommandWorkflow

public CommandWorkflow(ExecutorArguments executionArguments,
                       CommandWorkflowModel workflowCommand,
                       List<Module> firstSteps,
                       List<Module> endSteps,
                       Design design)
                throws EoulsanException

Public constructor.

Parameters:

executionArguments - execution arguments

workflowCommand - Command object with the content of the parameter file

firstSteps - optional steps to add at the beginning of the workflow

endSteps - optional steps to add at the end of the workflow

design - Design to use with the workflow

Throws:

EoulsanException - if the creation of the CommandWorkflow object fails

Method Detail

saveConfigurationFiles

protected void saveConfigurationFiles()
                               throws EoulsanException

Description copied from class: AbstractWorkflow

Save configuration files.

Overrides:

saveConfigurationFiles in class AbstractWorkflow

Throws:

EoulsanException - if an error while writing files