Writing rds files as log can crash Snakemake execution

[votti]

I noticed that this workflow often saves the snakemake object as a log output as rds objects.

Unfortunately in some snakemake configurations (ie a setting/executor that uses --show-failed-logs) this causes the whole workflow execution to crash.

The error is something in the line of:

  File "<frozen codecs>", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 0: invalid start byte

This has been reported to snakemake (snakemake/snakemake#2826) and I have authored a fix (snakemake/snakemake#2827).