We've moved!
For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.

CWL workflow fails running locally

I have a CWL workflow, the files are here:


I can run it just fine using cwltool/cwl-runner as follows:

cwl-runner bwa-memWorkflow.cwl localInputs.yml

When I try and run it with cromwell I get an error that "The job was aborted from outside Cromwell" but I definitely did not abort it myself.

Here is the command I used to run this workflow in Cromwell:

java -jar cromwell-36.jar  run bwa-memWorkflow.cwl -i localInputs.yml -p bwa-pe.cwl.zip

(bwa-pe.cwl.zip just contains the dependency bwa-pe.cwl)

And here's the full output of it:


My ultimate goal is to switch over to the AWS Batch back end (in case you are wondering why I don't just stick with cwltool) but first I wanted to get the workflow running locally in cromwell.

Any ideas about this?


Sign In or Register to comment.