Could not find suitable filesystem among Default to parse

Hello,

I have a hello world wdl as follows:

task helloWorld {
    File infile
    String name
    Int sleep
    command {
    sleep ${sleep}
    echo "Writing to file..."
    date >> ${infile}
    echo Hello, ${name} >> ${infile}
    } output {
    File outfile = "${infile}"
    } runtime {
     docker : "gcr.io/btl-dockers/btl_gatk:1"
 }
}


workflow hello {
    File infile
    File fofn
    String name
    Int sleep
    scatter(row in read_tsv(fofn)) {
        call helloWorld {
        input:
            infile = row[1],
            name = row[0],
            sleep = sleep
        }
    }
}

I've passed an input json file that has some files in it:

{
  "hello.name": "amr",
  "hello.out": "hello.txt",
  "hello.sleep": 1,
  "hello.infile": "D:\\Dev\\Python\\widdler\\resources\\hello_input.txt",
  "hello.fofn": "D:\\Dev\\Python\\widdler\\resources\\hello.fofn"
}

I've launched a cromwell server as follows:

java -jar D:\Dev\cromwell-30.2.jar server

When I try to execute the WDL above, I get the following error, which seems to suggest Cromwell is unable to parse my local file system path.

2018-02-20 10:27:09,755 cromwell-system-akka.dispatchers.api-dispatcher-53 INFO  - Workflow 0f63b8e3-e927-48ce-aa84-22a82d5cdefc submitted.
2018-02-20 10:27:22,125 cromwell-system-akka.dispatchers.engine-dispatcher-26 INFO  - 1 new workflows fetched
2018-02-20 10:27:22,126 cromwell-system-akka.dispatchers.engine-dispatcher-26 INFO  - WorkflowManagerActor Starting workflow UUID(0f63b8e3-e927-48ce-aa84-22a82d5cdefc)
2018-02-20 10:27:22,132 cromwell-system-akka.dispatchers.engine-dispatcher-26 INFO  - WorkflowManagerActor Successfully started WorkflowActor-0f63b8e3-e927-48ce-aa84-22a82d5cdefc
2018-02-20 10:27:22,132 cromwell-system-akka.dispatchers.engine-dispatcher-26 INFO  - Retrieved 1 workflows from the WorkflowStoreActor
2018-02-20 10:27:22,818 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - MaterializeWorkflowDescriptorActor [UUID(0f63b8e3)]: Call-to-Backend assignments: hello.helloWorld -> Local
2018-02-20 10:27:25,006 cromwell-system-akka.dispatchers.engine-dispatcher-27 ERROR - Failed to delete workflow log
java.nio.file.FileSystemException: D:\Dev\cromwell-workflow-logs\workflow.0f63b8e3-e927-48ce-aa84-22a82d5cdefc.log: The process cannot access the file because it is being used by another process.

        at sun.nio.fs.WindowsException.translateToIOException(Unknown Source)
        at sun.nio.fs.WindowsException.rethrowAsIOException(Unknown Source)
        at sun.nio.fs.WindowsException.rethrowAsIOException(Unknown Source)
        at sun.nio.fs.WindowsFileSystemProvider.implDelete(Unknown Source)
        at sun.nio.fs.AbstractFileSystemProvider.delete(Unknown Source)
        at java.nio.file.Files.delete(Unknown Source)
        at better.files.File.delete(File.scala:619)
        at cromwell.core.path.BetterFileMethods.delete(BetterFileMethods.scala:413)
        at cromwell.core.path.BetterFileMethods.delete$(BetterFileMethods.scala:412)
        at cromwell.core.path.DefaultPath.delete(DefaultPathBuilder.scala:55)
        at cromwell.core.logging.WorkflowLogger.$anonfun$deleteLogFile$2(WorkflowLogger.scala:111)
        at scala.Option.foreach(Option.scala:257)
        at cromwell.core.logging.WorkflowLogger.$anonfun$deleteLogFile$1(WorkflowLogger.scala:111)
        at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
        at scala.util.Try$.apply(Try.scala:209)
        at cromwell.core.logging.WorkflowLogger.deleteLogFile(WorkflowLogger.scala:111)
        at cromwell.engine.workflow.WorkflowActor$$anonfun$8.applyOrElse(WorkflowActor.scala:413)
        at cromwell.engine.workflow.WorkflowActor$$anonfun$8.applyOrElse(WorkflowActor.scala:378)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
        at akka.actor.FSM.$anonfun$handleTransition$1(FSM.scala:608)
        at akka.actor.FSM.$anonfun$handleTransition$1$adapted(FSM.scala:608)
        at scala.collection.immutable.List.foreach(List.scala:389)
        at akka.actor.FSM.handleTransition(FSM.scala:608)
        at akka.actor.FSM.makeTransition(FSM.scala:690)
        at akka.actor.FSM.makeTransition$(FSM.scala:683)
        at cromwell.engine.workflow.WorkflowActor.makeTransition(WorkflowActor.scala:181)
        at akka.actor.FSM.applyState(FSM.scala:675)
        at akka.actor.FSM.applyState$(FSM.scala:673)
        at cromwell.engine.workflow.WorkflowActor.applyState(WorkflowActor.scala:181)
        at akka.actor.FSM.processEvent(FSM.scala:670)
        at akka.actor.FSM.processEvent$(FSM.scala:662)
        at cromwell.engine.workflow.WorkflowActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowActor.scala:181)
        at akka.actor.LoggingFSM.processEvent(FSM.scala:801)
        at akka.actor.LoggingFSM.processEvent$(FSM.scala:783)
        at cromwell.engine.workflow.WorkflowActor.processEvent(WorkflowActor.scala:181)
        at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:659)
        at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:653)
        at akka.actor.Actor.aroundReceive(Actor.scala:514)
        at akka.actor.Actor.aroundReceive$(Actor.scala:512)
        at cromwell.engine.workflow.WorkflowActor.aroundReceive(WorkflowActor.scala:181)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
        at akka.actor.ActorCell.invoke(ActorCell.scala:496)
        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 akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
2018-02-20 10:27:25,009 cromwell-system-akka.dispatchers.engine-dispatcher-6 ERROR - WorkflowManagerActor Workflow 0f63b8e3-e927-48ce-aa84-22a82d5cdefc failed (during ExecutingWorkflowState): Evaluating read_tsv(fofn) failed: java.lang.IllegalArgumentException: Could not find suitable filesystem among Default to parse D:\Dev\Python\widdler\resources\h
ello.fofn.
java.lang.RuntimeException: Evaluating read_tsv(fofn) failed: java.lang.IllegalArgumentException: Could not find suitable filesystem among Default to parse D:\Dev\Python\widdler\resources\hello.fofn.
        at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.$anonfun$processRunnable$2(ExpressionKey.scala:36)
        at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.$anonfun$processRunnable$2$adapted(ExpressionKey.scala:31)
        at scala.Function1.$anonfun$andThen$1(Function1.scala:52)
        at cats.data.Validated.fold(Validated.scala:14)
        at cats.data.Validated.bimap(Validated.scala:109)
        at cats.data.Validated.map(Validated.scala:152)
        at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.processRunnable(ExpressionKey.scala:31)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$startRunnableNodes$4(WorkflowExecutionActor.scala:422)
        at cats.instances.ListInstances$$anon$1.$anonfun$traverse$2(list.scala:65)
        at cats.instances.ListInstances$$anon$1.loop$2(list.scala:58)
        at cats.instances.ListInstances$$anon$1.$anonfun$foldRight$2(list.scala:60)
        at cats.Eval$Call$.cats$Eval$Call$$loop(Eval.scala:267)
        at cats.Eval$Call.value(Eval.scala:257)
        at cats.instances.ListInstances$$anon$1.traverse(list.scala:64)
        at cats.instances.ListInstances$$anon$1.traverse(list.scala:12)
        at cats.Traverse$Ops.traverse(Traverse.scala:19)
        at cats.Traverse$Ops.traverse$(Traverse.scala:19)
        at cats.Traverse$ToTraverseOps$$anon$3.traverse(Traverse.scala:19)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.cromwell$engine$workflow$lifecycle$execution$WorkflowExecutionActor$$startRunnableNodes(WorkflowExecutionActor.scala:416)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:148)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:146)
        at scala.PartialFunction$OrElse.apply(PartialFunction.scala:168)
        at akka.actor.FSM.processEvent(FSM.scala:668)
        at akka.actor.FSM.processEvent$(FSM.scala:662)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowExecutionActor.scala:41)
        at akka.actor.LoggingFSM.processEvent(FSM.scala:801)
        at akka.actor.LoggingFSM.processEvent$(FSM.scala:783)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.processEvent(WorkflowExecutionActor.scala:41)
        at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:659)
        at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:653)
        at akka.actor.Actor.aroundReceive(Actor.scala:514)
        at akka.actor.Actor.aroundReceive$(Actor.scala:512)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$Timers$$super$aroundReceive(WorkflowExecutionActor.scala:41)
        at akka.actor.Timers.aroundReceive(Timers.scala:40)
        at akka.actor.Timers.aroundReceive$(Timers.scala:36)
        at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.aroundReceive(WorkflowExecutionActor.scala:41)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
        at akka.actor.ActorCell.invoke(ActorCell.scala:496)
        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 akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

2018-02-20 10:27:25,011 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - WorkflowManagerActor WorkflowActor-0f63b8e3-e927-48ce-aa84-22a82d5cdefc is in a terminal state: WorkflowFailedState

Does Cromwell require a config file in order to operate in a Windows file system environment? Any help getting past this issue appreciated!

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