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

Class CommandWorkflowModel

  • All Implemented Interfaces:
    Serializable
    public class CommandWorkflowModel
extends Object
implements Serializable
    This class define the workflow model object of Eoulsan.
    Since:
    1.0
    Author:
    Laurent Jourdren
    See Also:
    Serialized Form

    • Constructor Detail

      • CommandWorkflowModel

        public CommandWorkflowModel()
        Public constructor.

      • CommandWorkflowModel

        public CommandWorkflowModel​(boolean addSettingsValues)
        Public constructor.
        Parameters:
        addSettingsValues - if all the settings must be added to global properties

    • Method Detail

      • getName

        public String getName()
        Get the name.
        Returns:
        Returns the name

      • getDescription

        public String getDescription()
        Get description.
        Returns:
        Returns the description

      • getAuthor

        public String getAuthor()
        Get Author.
        Returns:
        Returns the author

      • getGlobalParameters

        public Set<Parameter> getGlobalParameters()
        Get the globals parameters.
        Returns:
        a set of globals parameters

      • getStepIds

        public List<String> getStepIds()
        Get the list of step ids.
        Returns:
        a list of step ids

      • getModuleName

        public String getModuleName​(String stepId)
        Get the module name of the step.
        Parameters:
        stepId - step id
        Returns:
        the name of the step

      • getStepVersion

        public String getStepVersion​(String stepId)
        Get the required version of the step.
        Parameters:
        stepId - step id
        Returns:
        the required version of the step

      • getStepInputs

        public Map<String,​fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel.StepPort> getStepInputs​(String stepId)
        Get the inputs of a step
        Parameters:
        stepId - the id of the step
        Returns:
        a Map of with the inputs of the step

      • getStepParameters

        public Set<Parameter> getStepParameters​(String stepId)
        Get the parameters of a step
        Parameters:
        stepId - the id of the step
        Returns:
        a set of the parameters of the step

      • isStepSkipped

        public boolean isStepSkipped​(String stepId)
        Test if the step is skipped.
        Parameters:
        stepId - step id
        Returns:
        true if the step is skipped

      • getStepDiscardOutput

        public Step.DiscardOutput getStepDiscardOutput​(String stepId)
        Get the discard output value.
        Parameters:
        stepId - step id
        Returns:
        the discard output value

      • getStepRequiredMemory

        public int getStepRequiredMemory​(String stepId)
        Get the required memory for the step.
        Parameters:
        stepId - step id
        Returns:
        the required memory of the step in MB or -1 if the default setting must be used

      • getStepRequiredProcessors

        public int getStepRequiredProcessors​(String stepId)
        Get the required processors for the step.
        Parameters:
        stepId - step id
        Returns:
        the required processors count for the step in MB or -1 if the default setting must be used

      • getStepDataProduct

        public String getStepDataProduct​(String stepId)
        Get the data product for the step.
        Parameters:
        stepId - step id
        Returns:
        the data product