Module: Cromwell

Defined in:
lib/rbbt/workflow/integration/cromwell.rb

Class Method Summary collapse

Class Method Details

.run_cromwell(file, work_dir, options = {}) ⇒ Object 



6
7
8
9
10
11
12
13
14
 
# File 'lib/rbbt/workflow/integration/cromwell.rb', line 6

def self.run_cromwell(file, work_dir, options = {})
  cromwell_inputs_file = Misc.process_options options, :cromwell_inputs_file
  jar = Rbbt.software.opt.jar["cromwell.jar"].produce.find
  if cromwell_inputs_file
    CMD.cmd_log("java -jar '#{jar}' run '#{file}' --workflow-root='#{work_dir}' -i #{cromwell_inputs_file}", options.merge("add_option_dashes" => true))
  else
    CMD.cmd_log("java -jar '#{jar}' run '#{file}' --workflow-root='#{work_dir}'", options.merge("add_option_dashes" => true))
  end
end