Class: Bio::Pipengine::Step

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/pipengine/step.rb

Overview

Step holds information for a pipeline step groups_def is used to store information on groups definition (i.e. generic cmd lines with placeholders) groups_cmd is used to store the actual command lines for all the samples to be combined in a “groups” step this are generated by combining groups_def information with sample groups information and will be placed where <groups> placeholder is found into the step command lines.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(name, step_instructions) ⇒ Step

Returns a new instance of Step.



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# File 'lib/bio/pipengine/step.rb', line 11

def initialize(name,step_instructions)
	@name = name
	parse_yaml(step_instructions)	
end

Instance Attribute Details

#cpus ⇒ Object

Returns the value of attribute cpus.



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# File 'lib/bio/pipengine/step.rb', line 10

def cpus
  @cpus
end

#mem ⇒ Object

Returns the value of attribute mem.



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# File 'lib/bio/pipengine/step.rb', line 10

def mem
  @mem
end

#multi_cmd ⇒ Object

Returns the value of attribute multi_cmd.



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# File 'lib/bio/pipengine/step.rb', line 10

def multi_cmd
  @multi_cmd
end

#multi_def ⇒ Object

Returns the value of attribute multi_def.



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# File 'lib/bio/pipengine/step.rb', line 10

def multi_def
  @multi_def
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/bio/pipengine/step.rb', line 10

def name
  @name
end

#nodes ⇒ Object

Returns the value of attribute nodes.



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# File 'lib/bio/pipengine/step.rb', line 10

def nodes
  @nodes
end

#pre ⇒ Object

Returns the value of attribute pre.



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# File 'lib/bio/pipengine/step.rb', line 10

def pre
  @pre
end

#run ⇒ Object

Returns the value of attribute run.



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# File 'lib/bio/pipengine/step.rb', line 10

def run
  @run
end

Instance Method Details

#has_prerequisite? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/pipengine/step.rb', line 20

def has_prerequisite?
	return (self.pre.nil?) ? false : true
end

#is_multi? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/pipengine/step.rb', line 16

def is_multi?
	return (self.multi_def.nil?) ? false : true
end