CODEWITHSUNDEEP
snakemake
yahan
yahan

Reputation: 81

can snakemake choose a config file based on a parameter?

I am building a snakemake workflow that will be used with different configurations.

Ideally I would be able to pass a parameter on commandline to determine which conf file to use.

I know how to pass a parameter e.g.

--config parameter=value

But as far as I can see this the gets added to the config dict.

So I can't define configfile using this parameter.

Thanks for your comments.

Upvotes: 1

Views: 396

Answers (1)

Russ Hyde
Russ Hyde

Reputation: 2269

Have you used --configfile. Provided you want to switch the choice of configfile at the command line, rather than within the snakemake run, this should be the argument you need.

Upvotes: 1

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