class Bio::Pipengine::Step
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.
Attributes
cpus[RW]
mem[RW]
multi_cmd[RW]
multi_def[RW]
name[RW]
nodes[RW]
pre[RW]
run[RW]
Public Class Methods
new(name,step_instructions)
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# File lib/bio/pipengine/step.rb, line 11 def initialize(name,step_instructions) @name = name parse_yaml(step_instructions) end
Public Instance Methods
has_prerequisite?()
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# File lib/bio/pipengine/step.rb, line 20 def has_prerequisite? return (self.pre.nil?) ? false : true end
is_multi?()
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# File lib/bio/pipengine/step.rb, line 16 def is_multi? return (self.multi_def.nil?) ? false : true end
Private Instance Methods
parse_yaml(step_instructions)
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# File lib/bio/pipengine/step.rb, line 26 def parse_yaml(step_instructions) self.cpus = step_instructions["cpu"].to_i self.nodes = step_instructions["nodes"] self.mem = step_instructions["mem"] self.run = step_instructions["run"] self.multi_def = step_instructions["multi"] self.pre = step_instructions["pre"] end