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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Writing `rds` files as log can crash Snakemake execution #535

Closed votti closed 3 weeks ago

votti commented 2 months ago

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 (https://github.com/snakemake/snakemake/issues/2826) and I have authored a fix (https://github.com/snakemake/snakemake/issues/2827).

votti commented 3 weeks ago

This has now been fixed in the latest Snakemake version.