Addressing issue #228 - Snakefile and Snakefile_data have been modified to get paths from the configuration file, whenever they can.
As discussed in issue #228 - we cannot remove any wildcards from any of these paths without also tweaking the rules themselves, but we can always rearrange them as we see fit. I've tested this out by inserting random path components at random places in each of the paths, and it gets picked up by snakemake (and the tests pass).
Note that this does not mean that there aren't paths that haven't (yet) been exposed in the config file - all of these are in Snakemake for model evaluation purposes (in the model_evaluation folder relative to output_dir). These can be pulled out into the config file at some point if needed, but perhaps we can add another issue on that.
sample_file in the config files was never used, so I've removed that. Also disabled an annoying warning for now since that overwhelms stdout.
Addressing issue #228 -
SnakefileandSnakefile_datahave been modified to get paths from the configuration file, whenever they can.As discussed in issue #228 - we cannot remove any wildcards from any of these paths without also tweaking the rules themselves, but we can always rearrange them as we see fit. I've tested this out by inserting random path components at random places in each of the paths, and it gets picked up by
snakemake(and the tests pass).Note that this does not mean that there aren't paths that haven't (yet) been exposed in the
configfile - all of these are inSnakemakefor model evaluation purposes (in themodel_evaluationfolder relative tooutput_dir). These can be pulled out into theconfigfile at some point if needed, but perhaps we can add another issue on that.sample_filein the config files was never used, so I've removed that. Also disabled an annoying warning for now since that overwhelms stdout.