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Description
Snakemake version: 6.15.5
When I run snakemake in cluster mode, if a rule has a parameter which is not serializable, it leads to all parameters being removed from the serialization in jobscript
Minimal example:
import numpy as np
rule all:
input: "a.txt"
rule first:
output: "a.txt"
params:
good="Good old value",
bad=np.int64(1)
shell:
"touch a.txt"
The output of snakemake --cluster sbatch -j1 --verbose prints the jobscript properties:
Jobscript:
#!/bin/sh
# properties = {"type": "single", "rule": "first", "local": false, "input": [], "output": ["a.txt"], "wildcards": {}, "log": [], "threads": 1, "resources": {"tmpdir": "/tmp"}, "jobid": 1, "cluster": {}}
I expect that the parameter definition will at least have the good serializable parameter. Ideally I would also like numpy types to serialize.
If maintainers are fine with fixing this at all, I can submit a pull request with the fix
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