Generally need to sort out WorkDir vs OutDir and what lives where.
Currently it's downloading reference genome stuff and making the master unzipped fna in WorkDir, but the reference DB is being made in pwd (no override argument).
~This means my validation code looking for an existing db in WorkDir is incorrect.~ fixed this.
I think ideally ~all the side-effect (non-output) files should live in WorkDir and~ the output should be in OutDir. The error log file (my redirected output from genome downloader) arguably should also live in OutDir, as the validation code will complain to stdout about any specified directories not existing - so we won't encounter errors trying to write to OutDir.
Generally need to sort out WorkDir vs OutDir and what lives where.
Currently it's downloading reference genome stuff and making the master unzipped fna in WorkDir, but the reference DB is being made in pwd (no override argument). ~This means my validation code looking for an existing db in WorkDir is incorrect.~ fixed this.
I think ideally ~all the side-effect (non-output) files should live in WorkDir and~ the output should be in OutDir. The error log file (my redirected output from genome downloader) arguably should also live in OutDir, as the validation code will complain to stdout about any specified directories not existing - so we won't encounter errors trying to write to OutDir.