We just need to make sure that all changes in the config result in changes in:
wildcards
parameters
or indirectly through input files
-> maybe pass all relevant config inputs to final output rule to force reruns (eventhough they are not used in that rule, but the ones producing its output. otherwise the rule won't be rerun as snakemake only checks immediate changes)
Should be addressed by this https://github.com/snakemake/snakemake/issues/1694
We just need to make sure that all changes in the config result in changes in:
-> maybe pass all relevant config inputs to final output rule to force reruns (eventhough they are not used in that rule, but the ones producing its output. otherwise the rule won't be rerun as snakemake only checks immediate changes)