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) click to toggle source
# 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?() click to toggle source
# File lib/bio/pipengine/step.rb, line 20
def has_prerequisite?
        return (self.pre.nil?) ? false : true
end
is_multi?() click to toggle source
# 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) click to toggle source
# 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