CODEWITHSUNDEEP
snakemake
sandro
sandro

Reputation: 21

Overwrite nested config options on command line

Is it possible to overwrite nested config options with Snakemake's --config command line option? For example: an option accessed internally with config['step_a']['opt_b']. Is there some syntax to specify this when starting the Snakemake workflow?

Upvotes: 1

Views: 488

Answers (1)

Robert Davy
Robert Davy

Reputation: 910

This works but you would need to supply other elements of the step_a dict:

--config "step_a={'opt_b':'c'}"

I think the proper way is to have a different config file using --configfile. If there is some config that is relatively static and some that is changeable, use two config files. You can supply multiple config files using --configfile.

Upvotes: 1

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