To my knowledge, when restarting a previously interrupted job that left behind incomplete files, Snakemake can:
a) --rerun-incomplete: i.e. treat the incomplete files as invalid, and rerun the saved command from the earlier run
b) --ignore-incomplete: i.e. treat the files marked as incomplete as complete and keep going
If our user cancels the job to adjust a subordinate config file, then neither of the options above are ideal. It would be nice for us to:
c) --remove-incomplete: i.e. remove the incomplete files from the filesystem and associated snakemake metadata, build a new command (with the new config), and run.
Is there an easy way to do this? (FYI we are using 3.7.1 and are open to upgrading.)
Snakemake rocks! Thanks!