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Invalid config definition error - version 8.17.0

Open lcoombe opened this issue 6 months ago • 0 comments

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?

lcoombe avatar Aug 13 '24 18:08 lcoombe