workflow = Workflow.find? template_uuid
if workflow.definition
begin
- wf_json = YAML::load(workflow.definition)
+ wf_json = ActiveSupport::HashWithIndifferentAccess.new YAML::load(workflow.definition)
rescue => e
logger.error "Error converting definition yaml to json: #{e.message}"
raise ArgumentError, "Error converting definition yaml to json: #{e.message}"
attrs['cwd'] = "/var/spool/cwl"
attrs['output_path'] = "/var/spool/cwl"
+ input_defaults = {}
+ if wf_json
+ inputs = get_cwl_inputs(wf_json)
+ inputs.each do |input|
+ if input[:default]
+ input_defaults[cwl_shortname(input[:id])] = input[:default]
+ end
+ end
+ end
+
# mounts
mounts = {
"/var/lib/cwl/cwl.input.json" => {
"kind" => "json",
- "content" => {}
+ "content" => input_defaults
},
"stdout" => {
"kind" => "file",