These two parameters in metadata validation were not fully connected throughout the pipeline, resulting in the user being unable to change their values.

The keep_demographic_info flag allows the user to elect to have potentially identifying metadata (host sex, age, race, ethnicity) removed from the metadata if present (keep_demographic_info=false should remove any data for the samples).

The date_format_flag flag allows the user to select a date format of YYYY-MM or YYYY-MM-DD (or to keep whatever is in the metadata).

Run environment (container, cloud service, HPC, platform, etc.)

Command to replicate the error:

Any Additional Context or Information?

These need to be added to the module files, the config files, and the nextflow_schema.json.

Their old implementation has different variable names (val_date_format and keep_personal_info), and the latter flag currently throws an error if demographic data is found the metadata and keep_personal_info = false.

I will change this implementation to instead just remove that data if found (and log what it has done).