For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.
issues submitting with the 'submit' subcommand of the cromwell jar file
I tried submitting a workflow like this:
java -jar cromwell-36.jar submit bwa-memWorkflow.cwl -i bwa-memWorkflowInputs.yml -p . -h http://localhost:8000
But got an error that '.' is a directory. However, the help (produced by java -jar cromwell-36.jar) says that the -p flag to the submit subcommand is " A directory or zipfile to search for workflow imports." Can either the help message or the functionality be changed so the two are consistent?
Different problem, here is another submit command:
java -jar 3-step-workflow/cromwell-36.jar submit workflows/wdl/hello_world_workflow.wdl -i inputs/hello_world_inputs.json -h http://fieldroast:8000
This actually submitted the job successfully as I could see from looking at the workflow status/metadata in the swagger UI given the workflow ID that the command returned.
However, the command returned a bunch of other output that looks like errors, and returned an error code of 130 instead of 0. All of this sort of obscured the fact that the workflow submission was successful.
Here is the output. Is this reporting an actual error that I as the end user need to know about?
[2018-12-21 11:26:06,81] [info] Slf4jLogger started [2018-12-21 11:26:08,87] [info] Workflow 374f1084-3041-460e-9385-817f894ee33b submitted to http://fieldroast:8000 [ERROR] [12/21/2018 11:26:08.934] [SubmitSystem-akka.actor.default-dispatcher-20] [akka://SubmitSystem/system/pool-master] connection pool for PoolGateway(hcps = HostConnectionPoolSetup(fieldroast,8000,ConnectionPoolSetup(ConnectionPoolSettings(4,0,5,32,1,30 seconds,ClientConnectionSettings(Some(User-Agent: akka-http/10.1.5),40 seconds,1 minute,512,None,WebSocketSettings(<function0>,ping,Duration.Inf,akka.http.impl.settings.WebSocketSettingsImpl$$$Lambda$444/[email protected]),List(),ParserSettings(2048,16,64,64,8192,64,8388608,8388608,256,1048576,Strict,RFC6265,true,Set(),Full,Error,Map(If-Range -> 0, If-Modified-Since -> 0, If-Unmodified-Since -> 0, default -> 12, Content-MD5 -> 0, Date -> 0, If-Match -> 0, If-None-Match -> 0, User-Agent -> 32),false,true,akka.util.ConstantFun$$$Lambda$297/[email protected],akka.util.ConstantFun$$$Lambda$297/[email protected],akka.util.ConstantFun$$$Lambda$298/[email protected]),None,TCPTransport),New,1 second),[email protected],[email protected]))) has shut down unexpectedly