I have a workflow that begins by downloading files from a public database, and then in subsequent steps processes these files to create several aggregated data tables.
I’m testing the workflow on a machine with no internet connection. I ran the preliminary data download steps on another machine and copied them over to this machine, and now I’m trying to run the rest of the workflow. When I run snakemake -np it reports that all of the data download jobs still need to be completed, even though the target files already exist. I’ve even marked these files as ancient() in the subsequent processing rules, but this doesn’t help.
How can I convince Snakemake that these jobs don’t need to be re-run?
Flag --reason prints the reason for each executed rule.