Missing categorical values in data.psam

[mvochteloo]

According to the imputation manual missing values in the input data.psam file should be noted as 'NA'.

Plink2 however expects a 'NONE' value for all categorical values that are missing, resulting in the error:
Error: '<COLUMN>' entry on line <LINE> of <FILE> is numerical/'NA', while earlier entries are categorical. (Case/control and quantitative phenotypes must all be numeric/'NA'. Categegorical phenotypes cannot be 'NA' --use e.g. 'NONE' to represent missing categorical values instead--or start with a number.)

However, assigning a 'NONE' value to e.g. Provided_Ancestry results in an error in the pre-flight checks of the Snakefile.

The pre-flight checks should perhaps distinguish their accepted representations of missing values for categorical and numerical columns in the data.psam file.