abs-files.wdl

workflow AbsoluteOutputFiles {
  call MakeFilesTask
}

task MakeFilesTask {

  command {
    mkdir -p /mnt/datastore/resultdata
    date > /mnt/datastore/resultdata/output
  }

  runtime {
    docker: "abs-file"
  }

  output {
    File date_output = "/mnt/datastore/resultdata/output"
  }
}

cromwell log

cromwell run abs-files.wdl -
[2016-11-01 21:09:50,63] [info] Slf4jLogger started
[2016-11-01 21:09:50,93] [info] RUN sub-command
[2016-11-01 21:09:50,93] [info]   WDL file: /home/ubuntu/cinder-data-mount/code/scratch-wdl/abs-files/abs-files.wdl
[2016-11-01 21:09:50,97] [info] SingleWorkflowRunnerActor: Submitting workflow
[2016-11-01 21:09:51,50] [info] Running with database db.url = jdbc:hsqldb:mem:91036ee1-520a-4b41-bb24-691532848ad8;shutdown=false;hsqldb.tx=mvcc
[2016-11-01 21:09:56,71] [info] Metadata summary refreshing every 2 seconds.
[2016-11-01 21:09:56,93] [info] Workflow 00413096-68f2-4f1f-9c64-ece620792668 submitted.
[2016-11-01 21:09:56,93] [info] SingleWorkflowRunnerActor: Workflow submitted 00413096-68f2-4f1f-9c64-ece620792668
[2016-11-01 21:09:57,04] [info] 1 new workflows fetched
[2016-11-01 21:09:57,04] [info] WorkflowManagerActor Starting workflow 00413096-68f2-4f1f-9c64-ece620792668
[2016-11-01 21:09:57,04] [info] WorkflowManagerActor Successfully started WorkflowActor-00413096-68f2-4f1f-9c64-ece620792668
[2016-11-01 21:09:57,04] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2016-11-01 21:09:57,19] [info] MaterializeWorkflowDescriptorActor [00413096]: Call-to-Backend assignments: AbsoluteOutputFiles.MakeFilesTask -> Local
[2016-11-01 21:09:57,33] [info] WorkflowExecutionActor-00413096-68f2-4f1f-9c64-ece620792668 [00413096]: Starting calls: AbsoluteOutputFiles.MakeFilesTask:NA:1
[2016-11-01 21:09:57,40] [info] SharedFileSystemAsyncJobExecutionActor [00413096AbsoluteOutputFiles.MakeFilesTask:NA:1]: mkdir -p /mnt/datastore/resultdata
date > /mnt/datastore/resultdata/output
[2016-11-01 21:09:57,41] [info] SharedFileSystemAsyncJobExecutionActor [00413096AbsoluteOutputFiles.MakeFilesTask:NA:1]: executing: docker run -v /home/ubuntu/data-mount/cromwell/exec/AbsoluteOutputFiles/00413096-68f2-4f1f-9c64-ece620792668/call-MakeFilesTask:/root/AbsoluteOutputFiles/00413096-68f2-4f1f-9c64-ece620792668/call-MakeFilesTask -i abs-file /bin/bash /root/AbsoluteOutputFiles/00413096-68f2-4f1f-9c64-ece620792668/call-MakeFilesTask/execution/script
[2016-11-01 21:09:57,42] [info] SharedFileSystemAsyncJobExecutionActor [00413096AbsoluteOutputFiles.MakeFilesTask:NA:1]: command: "/bin/bash" "/home/ubuntu/data-mount/cromwell/exec/AbsoluteOutputFiles/00413096-68f2-4f1f-9c64-ece620792668/call-MakeFilesTask/execution/script.submit"
[2016-11-01 21:09:57,43] [info] SharedFileSystemAsyncJobExecutionActor [00413096AbsoluteOutputFiles.MakeFilesTask:NA:1]: job id: 22023
[2016-11-01 21:10:01,79] [error] WorkflowManagerActor Workflow 00413096-68f2-4f1f-9c64-ece620792668 failed (during ExecutingWorkflowState): wdl4s.util.AggregatedException: Workflow 00413096-68f2-4f1f-9c64-ece620792668 post processing failed.Could not process output, file not found: /mnt/datastore/resultdata/output
[2016-11-01 21:10:01,79] [info] WorkflowManagerActor WorkflowActor-00413096-68f2-4f1f-9c64-ece620792668 is in a terminal state: WorkflowFailedState
[2016-11-01 21:10:04,39] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2016-11-01 21:10:04,39] [error] Workflow 00413096-68f2-4f1f-9c64-ece620792668 transitioned to state Failed
java.lang.RuntimeException: Workflow 00413096-68f2-4f1f-9c64-ece620792668 transitioned to state Failed
	at cromwell.engine.workflow.SingleWorkflowRunnerActor$RunnerData.addFailure(SingleWorkflowRunnerActor.scala:51)
	at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:128)
	at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:106)
	at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
	at akka.actor.FSM$class.processEvent(FSM.scala:663)
	at cromwell.engine.workflow.SingleWorkflowRunnerActor.akka$actor$LoggingFSM$$super$processEvent(SingleWorkflowRunnerActor.scala:68)
	at akka.actor.LoggingFSM$class.processEvent(FSM.scala:799)
	at cromwell.engine.workflow.SingleWorkflowRunnerActor.processEvent(SingleWorkflowRunnerActor.scala:68)
	at akka.actor.FSM$class.akka$actor$FSM$$processMsg(FSM.scala:657)
	at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:651)
	at akka.actor.Actor$class.aroundReceive(Actor.scala:484)
	at cromwell.server.CromwellRootActor.aroundReceive(CromwellRootActor.scala:26)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:526)
	at akka.actor.ActorCell.invoke(ActorCell.scala:495)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
	at akka.dispatch.Mailbox.run(Mailbox.scala:224)
	at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
	at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Workflow 00413096-68f2-4f1f-9c64-ece620792668 transitioned to state Failed

file exists test

buchanan01 abs-files
docker run -it --volumes-from b265789b88ae ubuntu bash
root@acaa356dec3a:/# ls /mnt/
datastore
root@acaa356dec3a:/# ls /mnt/datastore/resultdata/output
/mnt/datastore/resultdata/output
root@acaa356dec3a:/# cat /mnt/datastore/resultdata/output
Tue Nov  1 21:10:00 UTC 2016
root@acaa356dec3a:/#