wm0ea-9ad:~ rmunshi$ cat sandbox/optional_task.wdl version 1.0 workflow my_workflow { input { File input_1 = "/Users/rmunshi/sandbox/optional_task.wdl" File? input_2 } call task1 { input: input_1 = input_1 } if (defined(input_2)) { call task2 { input: input_2 = task1.output_1 } } output { File output_1 = task1.output_1 File? output_2 = task2.output_2 } } task task1 { input { File input_1 } command { echo "Hello, world!" > hello.txt } output { File output_1 = "hello.txt" } } task task2 { input { File input_2 } command { cat ${input_2} > goodbye.txt } output { File output_2 = "goodbye.txt" } } wm0ea-9ad:~ rmunshi$ java -jar ~/cromwell-jars/cromwell-36.jar run ~/sandbox/optional_task.wdl [2018-12-21 16:41:53,08] [info] Running with database db.url = jdbc:hsqldb:mem:b6895020-20f8-41c2-9bbe-42913262b461;shutdown=false;hsqldb.tx=mvcc [2018-12-21 16:41:59,09] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 [2018-12-21 16:41:59,10] [info] [RenameWorkflowOptionsInMetadata] 100% [2018-12-21 16:41:59,19] [info] Running with database db.url = jdbc:hsqldb:mem:ed1424c5-e909-4cc0-9f84-0b1428649798;shutdown=false;hsqldb.tx=mvcc [2018-12-21 16:41:59,52] [info] Slf4jLogger started [2018-12-21 16:41:59,79] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-8e4a110", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2018-12-21 16:41:59,82] [info] Metadata summary refreshing every 2 seconds. [2018-12-21 16:41:59,85] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2018-12-21 16:41:59,85] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2018-12-21 16:41:59,85] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2018-12-21 16:42:00,45] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2018-12-21 16:42:00,46] [info] SingleWorkflowRunnerActor: Version 36 [2018-12-21 16:42:00,47] [info] SingleWorkflowRunnerActor: Submitting workflow [2018-12-21 16:42:00,50] [info] Unspecified type (Unspecified version) workflow 19dd7212-4d18-4aee-ad92-5cb0b7a624d4 submitted [2018-12-21 16:42:00,52] [info] SingleWorkflowRunnerActor: Workflow submitted 19dd7212-4d18-4aee-ad92-5cb0b7a624d4 [2018-12-21 16:42:00,52] [info] 1 new workflows fetched [2018-12-21 16:42:00,52] [info] WorkflowManagerActor Starting workflow 19dd7212-4d18-4aee-ad92-5cb0b7a624d4 [2018-12-21 16:42:00,52] [info] WorkflowManagerActor Successfully started WorkflowActor-19dd7212-4d18-4aee-ad92-5cb0b7a624d4 [2018-12-21 16:42:00,53] [info] Retrieved 1 workflows from the WorkflowStoreActor [2018-12-21 16:42:00,53] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData [2018-12-21 16:42:00,54] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2018-12-21 16:42:00,60] [info] MaterializeWorkflowDescriptorActor [19dd7212]: Parsing workflow as WDL 1.0 [2018-12-21 16:42:01,33] [info] MaterializeWorkflowDescriptorActor [19dd7212]: Call-to-Backend assignments: my_workflow.task2 -> Local, my_workflow.task1 -> Local [2018-12-21 16:42:03,81] [info] WorkflowExecutionActor-19dd7212-4d18-4aee-ad92-5cb0b7a624d4 [19dd7212]: Starting my_workflow.task1 [2018-12-21 16:42:04,59] [info] BackgroundConfigAsyncJobExecutionActor [19dd7212my_workflow.task1:NA:1]: echo "Hello, world!" > hello.txt [2018-12-21 16:42:04,63] [info] BackgroundConfigAsyncJobExecutionActor [19dd7212my_workflow.task1:NA:1]: executing: /bin/bash /Users/rmunshi/cromwell-executions/my_workflow/19dd7212-4d18-4aee-ad92-5cb0b7a624d4/call-task1/execution/script [2018-12-21 16:42:04,89] [info] BackgroundConfigAsyncJobExecutionActor [19dd7212my_workflow.task1:NA:1]: job id: 62533 [2018-12-21 16:42:04,89] [info] BackgroundConfigAsyncJobExecutionActor [19dd7212my_workflow.task1:NA:1]: Status change from - to Done [2018-12-21 16:42:06,89] [info] WorkflowExecutionActor-19dd7212-4d18-4aee-ad92-5cb0b7a624d4 [19dd7212]: Workflow my_workflow complete. Final Outputs: { "my_workflow.output_2": null, "my_workflow.output_1": "/Users/rmunshi/cromwell-executions/my_workflow/19dd7212-4d18-4aee-ad92-5cb0b7a624d4/call-task1/execution/hello.txt" } [2018-12-21 16:42:06,91] [info] WorkflowManagerActor WorkflowActor-19dd7212-4d18-4aee-ad92-5cb0b7a624d4 is in a terminal state: WorkflowSucceededState