brentp
commented
6 years ago I see the utility of this in theory, but I won't implement. The main reason is to avoid adding more complexity to the user.
You can always just use -base-path and then symlink whatever files are needed into that base-path. That's just as easy for the user with less chance of being confusing.
In addition, since the conf is a simple text file, you can choose to make that a template and fill it with e.g. python and then send the resulting file to vcfanno.
Rather than hardcode the annotation file paths in the config file, I'd like to be able to put a placeholder in the config file and pass the actual paths on the command line. The use case is when vcfanno is used in a fully reproducible pipeline in which the annotation file may be downloaded to a temporary location, and thus the file paths are not known ahead of time. I'm envisioning something like this: