Snakemake version
9.11.4
Describe the bug
configfile: in module's Snakefile raises error if no config: in module declaration
The Modules documentation implies that a module should use its own configuration unless the module declaration specifies a config: argument:
It is possible to overwrite the global config dictionary for the module, which is usually filled by the configfile statement (see Standard Configuration):
...
In this case, any configfile statements inside the module are ignored.
Logs
KeyError in file ".../../workflow2/Snakefile", line 1:
'config'
Minimal example
.
├── config
│ └── config.yml
├── workflow
│ └── Snakefile
├── workflow1
│ ├── config
│ │ └── config.yml
│ └── Snakefile
└── workflow2
├── config
│ └── config.yml
└── Snakefile
# workflow/Snakefile
from snakemake.utils import min_version
min_version("6.0")
configfile: "config/config.yml"
module workflow1:
snakefile: "../workflow1/Snakefile"
config: config["config1"]
use rule * from workflow1 as workflow1_*
module workflow2:
snakefile: "../workflow2/Snakefile"
use rule * from workflow2 as workflow2_*
# workflow1/Snakefile
configfile: "config/config.yml"
# workflow2/Snakefile
configfile: "config/config.yml"
Additional context
Snakemake version
9.11.4
Describe the bug
configfile:in module's Snakefile raises error if noconfig:in module declarationThe Modules documentation implies that a module should use its own configuration unless the module declaration specifies a
config:argument:Logs
Minimal example
Additional context