File Override

[s-canchi]

Can you override if you wanted to overwrite the exiting file?
Related: Does snakemake only check if the file exists ? Is there a way to check if it's a certain size, etc.. since file metadata can change.

[marisalim]

There are a few snakemake flag options that allow you to write over existing files (i.e., see this FAQ answer):

  --force, -f           Force the execution of the selected target or the first rule regardless of already
                        created output.
  --forceall, -F        Force the execution of the selected (or the first) rule and all rules it is dependent on
                        regardless of already created output.
  --forcerun [TARGET ...], -R [TARGET ...]
                        Force the re-execution or creation of the given rules or files. Use this option if you
                        changed a rule and want to have all its output in your workflow updated.