No such file or directory while running python script in wdl

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Manish Gupta

• March 27, 2021 07:37

I am newbie to WDL world and trying my first program by wriitng first wdl and calling python script.

myworkflow.wdl

workflow myWorkflow {

    call myTask
}

task myTask {
    command {
        python3 ./script.py
    }
    output {
        String out = read_string(stdout())
    }
}

and script.py

#!/usr/bin/python3
print("hello world")

Command for running workflow.jar

java -jar cromwell-58.jar run myWorkflow.wdl

but i am getting error message while running above command.

/usr/local/bin/python3: can't open file '/Users/myuser/wdl/cromwell/cromwell-executions/myWorkflow/6609f4d3-c8f2-4ede-8b60-f570994c6d8a/call-myTask/execution/./script.py: [Errno 2] No such file or directory

While mywokflow.wdl, script.py and cromwell-58.jar are in same folder. How can i fix such issue?

0

• 

  Sushma Chaluvadi

  • March 29, 2021 13:16

  Hi there!
  Can you try removing the `./` in front of `script.py` and see if that eliminates the error that you are getting. 

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