Peter Van Dyken

`None` would be the default if the cli param is not passed at all. E.g the three alternatives are: ``` 1. mycli 2. mycli --arg 3. mycli --arg param ```...

Hmm, interesting. This is getting a bit complicated, so I went ahead and wrote up mappings of all the possibilities. First, I'll restate my goal here as getting a clear,...

If we went with what I originally proposed, you would need to explicitly set it to `field("some default", nargs="?")`. Otherwise it wouldn't be possible. I'm not at all married to...

Sure thing. @cmeesters, I think this is more in your ballpark

@lhennig, until a proper solution to this is made, it's worth knowing that `shadow_prefix` can be edited from within the workflow: ``` workflow.shadow_prefix = some_function_to_edit_the_prefix(workflow.shadow_prefix) ``` The exact implementation of...

@vdechand, can you set your `--shadow` prefix in the CLI to some environment variable, then evaluate the variable in the workflow using `os.environ`? Have a function that checks if the...

So the workflow gets re-evaluated when jobs are submitted to the cluster, so the key is to have a function in your workflow that detects whether it's being run on...

My opinion would be to have a `--shadow-prefix-envvar` or similar that can be set to an environment variable. Snakemake would first attempt to read that, then if it doesn't exist,...

The env var option I propose would be re-evaluated in every job context. To be clear, the syntax would be ``` snakemake --shadow-prefix-envvar TMPDIR ``` With no '$'. I think...

> This workaround is not working anymore (snakemake==8.10.8) due to: > ``` > AttributeError in file [...] > 'Workflow' object has no attribute 'run_local' > ``` The API was completely...