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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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Manually overriding stages within a pipeline? #449

Closed dorkylever closed 4 years ago

dorkylever commented 4 years ago

Hi Everyone,

In to relation to https://github.com/Mouse-Imaging-Centre/pydpiper/issues/448; Is it possible to manually correct stages after a pipeline is initialised?

Kind Regards, Kyle Drover

bcdarwin commented 4 years ago

In principle you could write some bash/Python/... script that given a command prints out a fixed version of that command and then install it in Pydpiper with --cmd-wrapper /path/to/script.py but I've never actually tried this. Some more convenient builtin functionality would be nice to have, certainly, but it'd still probably operate at the level of the whole pipeline like this?

dorkylever commented 4 years ago

I think I have a fix but I need to test it fully. I'll make a pull request if it works.