Using a default config file while defining another via `--configfile` (that shares variables) [Snakemake]

Question

I have a default config file that defines all of the variables necessary to run my workflow. It is included using the line configfile: 'config/defaults.yaml' in the Snakemake file. I would like to then give another configuration at runtime via the --configfile switch, which could overwrite some of these default values. This would be handy for two reasons:

I can define only a subset of the configuration variable in the runtime configfile.
Bash completion no longer complains about undefined values when I tab complete, rendering tab completion useless due to the garbage error message.

Is this sort of thing possible? The current behavior seems to disregard the values given in the runtime --configfile.

krumpelstiltskin · Accepted Answer · 2024-08-22 17:52:21Z

1

Well, it appears as though snakemake acts in the expected manner, where the variables given using --configfile overwrite the variables given in the configfile: line.

answered Aug 22, 2024 at 17:52

krumpelstiltskin

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Using a default config file while defining another via `--configfile` (that shares variables) [Snakemake]

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