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cromwell CWL Workflow input processing failed

Recently, I used cromwell to run my CWL workflow, but always get error information like "Workflow input processing failed". It is weird because I can run successfully for each step of the workflow, but It always gets errors if I put all the steps together into one CWL workflow.

So I show you a very simple CWL workflow which runs tar and gzip for a file. I can successfully run this tar+gzip workflow using cwltool and Toil, but I get error when cromwell is used. I will appreciate if you can provide any suggestion. Thanks!

The input of yml file (I try json format too, but it still gets failed) is:

tar_input:
class: File
path : CCLE-HCC1143.vcf

The CWL workflow is:

class: Workflow
cwlVersion: v1.0
id: guogw86/temporaryproject/tar_gzip/5
label: tar_gzip
$namespaces:
sbg: 'https://sevenbridges.com'
inputs:
- id: tar_input
type: File
'sbg:x': -430
'sbg:y': 7
outputs:
- id: output
outputSource:
- gzip/output
type: File?
'sbg:x': 163
'sbg:y': 3.5
steps:
- id: tar
in:
- id: tar_input
source: tar_input
out:
- id: output_tar
run:
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
id: guogw86/temporaryproject/tar/4
baseCommand:
- cp
inputs:
- id: tar_input
type: File
inputBinding:
position: 0
shellQuote: false
outputs:
- id: output_tar
type: File
outputBinding:
glob: '.tar'
label: tar
arguments:
- position: 1
prefix: ''
shellQuote: false
valueFrom: copy_tar_input.txt
- position: 2
prefix: ''
shellQuote: false
valueFrom: '${ return "&& tar -cf tar_out.tar copy_tar_input.txt"}'
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
'sbg:projectName': temporaryproject
'sbg:revisionsInfo':
- 'sbg:revision': 0
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564244135
'sbg:revisionNotes': null
- 'sbg:revision': 1
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564244990
'sbg:revisionNotes': setup
- 'sbg:revision': 2
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564261275
'sbg:revisionNotes': version2
- 'sbg:revision': 3
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564265103
'sbg:revisionNotes': version3
- 'sbg:revision': 4
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564265448
'sbg:revisionNotes': version4
'sbg:image_url': null
'sbg:appVersion':
- v1.0
'sbg:id': guogw86/temporaryproject/tar/4
'sbg:revision': 4
'sbg:revisionNotes': version4
'sbg:modifiedOn': 1564265448
'sbg:modifiedBy': guogw86
'sbg:createdOn': 1564244135
'sbg:createdBy': guogw86
'sbg:project': guogw86/temporaryproject
'sbg:sbgMaintained': false
'sbg:validationErrors': []
'sbg:contributors':
- guogw86
'sbg:latestRevision': 4
'sbg:publisher': sbg
'sbg:content_hash': a3e453248fc96e15bcaf335e27468dbb9124eb7adfdf0b20d16a7a9637624ca3f
label: tar
'sbg:x': -236
'sbg:y': -36
- id: gzip
in:
- id: gzip_input
source: tar/output_tar
out:
- id: output
run:
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
id: guogw86/temporaryproject/gzip/7
baseCommand:
- cp
inputs:
- id: gzip_input
type: File
inputBinding:
position: 0
shellQuote: false
outputs:
- id: output
type: File?
outputBinding:
glob: '
.gz'
label: gzip
arguments:
- position: 1
prefix: ''
shellQuote: false
valueFrom: '${ return "./"}'
- position: 2
prefix: ''
shellQuote: false
valueFrom: '${ return "&& gzip tar_out.tar"}'
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
'sbg:projectName': temporaryproject
'sbg:revisionsInfo':
- 'sbg:revision': 0
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564245001
'sbg:revisionNotes': null
- 'sbg:revision': 1
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564245160
'sbg:revisionNotes': setup
- 'sbg:revision': 2
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564245441
'sbg:revisionNotes': vesion2
- 'sbg:revision': 3
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564246377
'sbg:revisionNotes': version3
- 'sbg:revision': 4
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564262744
'sbg:revisionNotes': no_output
- 'sbg:revision': 5
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564263143
'sbg:revisionNotes': version5
- 'sbg:revision': 6
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564265469
'sbg:revisionNotes': version6
- 'sbg:revision': 7
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564265583
'sbg:revisionNotes': version7
'sbg:image_url': null
'sbg:appVersion':
- v1.0
'sbg:id': guogw86/temporaryproject/gzip/7
'sbg:revision': 7
'sbg:revisionNotes': version7
'sbg:modifiedOn': 1564265583
'sbg:modifiedBy': guogw86
'sbg:createdOn': 1564245001
'sbg:createdBy': guogw86
'sbg:project': guogw86/temporaryproject
'sbg:sbgMaintained': false
'sbg:validationErrors': []
'sbg:contributors':
- guogw86
'sbg:latestRevision': 7
'sbg:publisher': sbg
'sbg:content_hash': ad2c4b4616e3f315279b2c954f8b3f74b8d9b47b41776c9bc8d40d44fbfe3d7fa
label: gzip
'sbg:x': -3
'sbg:y': 12
requirements: []
'sbg:projectName': temporaryproject
'sbg:revisionsInfo':
- 'sbg:revision': 0
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564245195
'sbg:revisionNotes': null
- 'sbg:revision': 1
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564245473
'sbg:revisionNotes': setup
- 'sbg:revision': 2
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564246584
'sbg:revisionNotes': version2
- 'sbg:revision': 3
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564261298
'sbg:revisionNotes': version3
- 'sbg:revision': 4
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564263239
'sbg:revisionNotes': version4
- 'sbg:revision': 5
'sbg:modifiedBy': guogw86
'sbg:modifiedOn': 1564265650
'sbg:revisionNotes': version5
'sbg:image_url': >-
https://cgc.sbgenomics.com/ns/brood/images/guogw86/temporaryproject/tar_gzip/5.png
'sbg:appVersion':
- v1.0
'sbg:id': guogw86/temporaryproject/tar_gzip/5
'sbg:revision': 5
'sbg:revisionNotes': version5
'sbg:modifiedOn': 1564265650
'sbg:modifiedBy': guogw86
'sbg:createdOn': 1564245195
'sbg:createdBy': guogw86
'sbg:project': guogw86/temporaryproject
'sbg:sbgMaintained': false
'sbg:validationErrors': []
'sbg:contributors':
- guogw86
'sbg:latestRevision': 5
'sbg:publisher': sbg
'sbg:content_hash': a350992a15696a35db7d41bf2c057b65c31ae4753361db83eb8f08d212de262cb

After I run "java -jar cromwell-44.jar run tar_gzip.cwl -i tar_gzip_job.yml", I get error:

2019-07-28 13:23:07,71] [error] WorkflowManagerActor Workflow 50701bf5-8549-4f4c-81a2-841672cdaf99 failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:

Invalid workflow reference: tar_gzip.cwl

at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:215)

at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:185)

at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:180)

at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)

at akka.actor.FSM.processEvent(FSM.scala:684)

at akka.actor.FSM.processEvent$(FSM.scala:681)

at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.akka$actor$LoggingFSM$$super$processEvent(MaterializeWorkflowDescriptorActor.scala:136)

at akka.actor.LoggingFSM.processEvent(FSM.scala:820)

at akka.actor.LoggingFSM.processEvent$(FSM.scala:802)

at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.processEvent(MaterializeWorkflowDescriptorActor.scala:136)

at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:678)

at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:672)

at akka.actor.Actor.aroundReceive(Actor.scala:517)

at akka.actor.Actor.aroundReceive$(Actor.scala:515)

at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.aroundReceive(MaterializeWorkflowDescriptorActor.scala:136)

at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)

at akka.actor.ActorCell.invoke(ActorCell.scala:557)

at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)

at akka.dispatch.Mailbox.run(Mailbox.scala:225)

at akka.dispatch.Mailbox.exec(Mailbox.scala:235)

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)
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