populate-jbrowse2: add refNameAliases when available

[nathanweeks]

Could the populate-jbrowse2 subcommand support per-assembly refNameAliases file (like the jbrowse add-assembly --refNameAliases option: https://jbrowse.org/jb2/docs/cli/#jbrowse-add-assembly-sequence)?

I'm not entirely sure what the CLI would look like. One suggestion is perhaps populate-jbrowse2 --refNameAliases_dir=<path>, where <path> is a path to a directory of refNameAliases TSV files named, e.g., <name>.txt; for each reference assembly name that is encountered in the yml config files, if <path>/<name>.txt exists, then a refNameAliases property is added to the output config.json. Could be other ways to implement this too.

[adf-ncgr]

Thanks @nathanweeks and sorry for the delayed response. It's a good idea, my initial reaction is that we ought to have a standardized (but optional) file resident in the datastore that iff present autocontent would just pass along as a URL for the --refNameAliases option value. I think that's pretty similar to what you suggested, except that there would be no option on the populate-jbrowse2 subcommand, it would just make it happen depending on the state of the datastore content. Would that work for your intended uses?

[adf-ncgr]

PS. IIRC, you can have a single tab-delimited file with multiple aliases per record, but if that isn't the case having a directory for these files as you suggested might be needed