Snakemake version
8.20.3

Describe the bug

When using cache: True on a rule with directory output, following the symlink to the .snakemake_timestamp on this line

https://github.com/snakemake/snakemake/blame/e9ce4a3c251d39efb02da0615c3b1210a475867d/snakemake/io.py#L527

results in a clock skew error if the input was files. The mtime of cached files do not follow the symlink ==> snakemake finds the input files are newer than the cached folder.

Logs
WorkflowError in rule A in file /pipeline/Snakefile, line 213:
Output folder_out has older modification time (2024-09-17 03:41:24.386847) than file_in (2024-09-17 10:35:20.241993). This could indicate a clock skew problem in your network and would trigger a rerun of this job in the next execution and should therefore be fixed on system level. System time: 2024-09-17 10:35:20.322207 (rule A, line 69, /pipeline/Snakefile)
Removing output files of failed job generate_salmon_index since they might be corrupted:
folder_out

Minimal example

A rule generating a cached folder with a cached file as input.

Additional context

Suggested (alternative) fixes:

• Do not follow the symlink. (Not sure if that has implications on other parts)
• Do not copy .snakemake_timestamp to/from the cache