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Invalid config definition error - version 8.17.0
Snakemake version version 8.17.0
Describe the bug
When I run my previously functional snakemake file, I get a ValueError:
ValueError: Invalid config definition: Config entry must start with a valid identifier.
I don't see the error with previous versions of snakemake, including 8.16.0
Logs
snakemake -s ntsynt_run_pipeline.smk -p --cores 12 --config references='['celegans-chrII-III.fa', 'celegans-chrII-III.A.fa']' k=24 w=1000 t=12 fpr=0.025 prefix=celegans-A-ntSynt w_rounds='100 10' indel_merge=500 collinear_merge=3000 block_size=500 common=True simplify_graph=True benchmark=False dev=False --resources load=2 --rerun-trigger mtime
Traceback (most recent call last):
File "/Users/miniconda3/envs/test/lib/python3.12/site-packages/snakemake/cli.py", line 1998, in args_to_api
config=parse_config(args.config),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/miniconda3/envs/test/lib/python3.12/site-packages/snakemake/cli.py", line 256, in parse_config
raise ValueError(
ValueError: Invalid config definition: Config entry must start with a valid identifier.
Additional context
It looks like this newest version doesn't allow for single character keys in the config? When I edited my makefile to use kmer
instead of k
, window
instead of w
and threads
instead of t
, I didn't see the error. I don't think that is expected behaviour, since that behaviour isn't backwards compatible?