config_extras_file argument

[Chris B]

I am interested in doing the run_analysis_pipeline with custom error_rate values for each sample (these are populated automatically in a new config.yaml file when run_analysis_pipeline is executed). Is there a way to specify them per sample in the config_extras_file or otherwise? Does someone have an example config_extras_file I could check for formatting (github repo doesn't have a template)?

Thanks!

Chris

[Andrew]

Hi Chris,

It is best to use the setup_analysis command and then manually change the resulting config file.

The --config_extras_file takes a yaml file with some of the (or all) of the sections in the normal config file. It will overwrite the default config sections with the ones in config_extras.

Cheers,

Andy