Add an option to create a filegraph in the dag rule

[tgilon]

Closes # (if applicable).

Changes proposed in this Pull Request

Checklist

• I tested my contribution locally and it works as intended.
• Code and workflow changes are sufficiently documented.
• Changed dependencies are added to envs/environment.yaml.
• Changes in configuration options are added in config/config.default.yaml.
• Changes in configuration options are documented in doc/configtables/*.csv.
• Sources of newly added data are documented in doc/data_sources.rst.
• A release note doc/release_notes.rst is added.

[fneum]

Nice utility! But avoid definition of dag_type outside rule definition.

It seems the current approach mixes two approaches (wildcards and parameters). With the current setup you could actually use

snakemake --{dag_type} all | sed -n "/digraph/,\$p" > {output.dot}

to run snakemake dag_filegraph.pdf or snakemake dag_rulegraph.pdf and forget about the params or config setting.

I would also be fine to just create both rulegraph and filegraph on run snakemake dag.

[fneum]

Suggested change

dag_type = config.get("dag_type", "rulegraph")

[fneum]

Suggested change

	dag_type=dag_type,
	dag_type=config.get("dag_type", "rulegraph"),

[tgilon]

Thanks @fneum for the review. Using only wildcards implies that we cannot have a default behaviour. That's why I suggest using config and a variable. I think the dag rule needs to be an easy to use rule as the dag is key to understanding the workflow (especially in the beginning).

# Not possible
snakemake dag

# Possible
snakemake resources/dag_rulegraph.pdf
snakemake resources/dag_filegraph.pdf

Also, as the filegraph may not be useful for everyone, I thought it would be a good idea to make it optional.

Would there be an implementation with wildcards and a default value?

[fneum]

Another option would be two separate rules:

snakemake rulegraph
snakemake filegraph