profile clashes with -- argument separator #3642
Description
Snakemake version: 9.6.1
Describe the bug
profile option clashes with -- argument separator.
Minimal example
Snakefile:
rule all:
input:
'done.txt',
rule one:
output:
'done.txt',
profile_tmp/config.yaml:
default-resources:
runtime: 10
slurm_account: project0061
This works fine:
snakemake -p -n --profile profile_tmp
Using profile profile_tmp for setting default command line arguments.
...
Now using --:
snakemake -p -n --profile profile_tmp -- done.txt
I get:
Using profile profile_tmp for setting default command line arguments.
host: login1.pri.mars.alces.network
Building DAG of jobs...
MissingRuleException:
No rule to produce slurm_account=project0061 (if you use input functions make sure that they don't raise unexpected exceptions).