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After a little investigation, this is actually a problem with the WDL command template generation: I'll tag this issue (PMCC-BioinformaticsCore/python-wdlgen#2) because I intend to fix this soon.
Hi Janis,
I think the tool is actually irrelevant, but I'm attaching it anyway. (oh. I can't attach Python? I'm pasting the code down the bottom.)
When I run:
Execution fails, and the following can be seen in the engine.log file:
It's obvious why this fails - the arguments are not being escaped.
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