The tool in its present state (i.e. v1.2.3) by default downloads an entire genome into the data/ directory if the users doesn't already have that information contained within this directory.
This is generally bad practice, as many different applications act on genomes, and it is not reasonable to expect a fresh download of genomes on an application-by-application basis. The same principle could perhaps be extended to other sequence data files currently used by FilTar. Instead, it would be better if genome files were discoverable by the application through the use of symbolic links
It would be for the best if some aspects of data download were made non-default unless explicitly requested by the user.
NB: One potential caveat is that it is not currently understood how snakemake acts upon symbolic links which would need to be explored.
NB: Another caveat is that effectively deautomating pre-alignment processes will increase the overhead to the user with respect to making sure that genome and annotations files match. Careful exception handling ought to be implemented here.
The tool in its present state (i.e. v1.2.3) by default downloads an entire genome into the data/ directory if the users doesn't already have that information contained within this directory.
This is generally bad practice, as many different applications act on genomes, and it is not reasonable to expect a fresh download of genomes on an application-by-application basis. The same principle could perhaps be extended to other sequence data files currently used by FilTar. Instead, it would be better if genome files were discoverable by the application through the use of symbolic links
It would be for the best if some aspects of data download were made non-default unless explicitly requested by the user.
NB: One potential caveat is that it is not currently understood how snakemake acts upon symbolic links which would need to be explored.
NB: Another caveat is that effectively deautomating pre-alignment processes will increase the overhead to the user with respect to making sure that genome and annotations files match. Careful exception handling ought to be implemented here.