Supressing stdout from noisy step in workflow

CWL Questions
1

I am currently writing a cwl specification that is effectively a wrapper for a python script. Even though I have rerouted stdout from within Python, I still get somewhere around 2 million output lines sent to the screen (likely because the library this tool uses is written in C, which does not follow the python redirect).

Although I have tried a number of ways to fix this at the python level, I was wondering if there was a way to suppress the output from a command at the cwl or docker image level? I can suppress the entire output if I pipe cwltool to a file, but I don’t want to do this further down the road when this cwl is one step in a workflow.

2

Oh. After stepping away from this for a bit I notice the answer was right in front of me in the documentation: an output object of type: stdout will capture and save that output in a file. A followup: is there a way to name this file, or are you stuck with the randomly generated one it gives you?

1 Like
3

Yep, use stdout: my_log_name and the same for stderr