work through all modules and add to the docs on config use (update: already added to the docs):
Now my recommendation is to NOT use any configs directly in scripts (or shell) but always via params so its traceable (provenance!). Otherwise, Snakemake can not notice a change in parameters and trigger a rerun. Sadly, my own modules do not adhere to it 100% yet as it was a later learning. Defining params for configs seems redundant but makes rules more readable/transparent and enables traceability for Snakemake.
related: snakemake/snakemake#1688
work through all modules and add to the docs on config use (update: already added to the docs):
Now my recommendation is to NOT use any configs directly in scripts (or shell) but always via
paramsso its traceable (provenance!). Otherwise, Snakemake can not notice a change in parameters and trigger a rerun. Sadly, my own modules do not adhere to it 100% yet as it was a later learning. Defining params for configs seems redundant but makes rules more readable/transparent and enables traceability for Snakemake.related: snakemake/snakemake#1688