Say I have a config.yaml file such as follows
results: "results/"
reference_database: "data/zymogen_alignment_file.fasta"
basecall:
perform_basecall: True
configuration: "dna_r9.4.1_450bps_hac.cfg"
I can access all the parameters in my Snakefile, such as config["results"]
, config["basecall"]["perform_basecall"]
, etc.
I can override the results
and reference_database
parameter easilysnakemake --cores all --config results="/my/new/results/path" reference_database="/my/new/reference/database"
However, I can't seem to be able to override the parameters under basecall
. I have tried the followingsnakemake --cores all --config basecall["perform_basecall"]=False
But this results in the error: Invalid config definition: Config entry must start with a valid identifier.
Is it possible to override parameters in a nested configuration file?
Thanks for any help!