module Cromwell
Public Class Methods
Source
# 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