Snakemake: Hiding certain rules from DAG visualisation

Question

In my snakemake pipeline, I have an 'all' rule, which located at the very bottom of the DAG of jobs. It's essentially the entry point for snakemake, but it doesn't do anything other than list all of the desired outputs.

Is there a way to hide this rule from the DAG visualization?

Answer 1

Running snakemake --dag generates a dot graph that can be modified as needed. For example:

snakemake --dag > test.dot
# edit test.dot to remove node 0 and all edges linking it
dot -Tpng test.dot -o test.png

In principle, editing of the dot file can also be automated using grep/sed/awk:

snakemake --dag | grep -v "> 0\|0\[label" | dot -Tpng -o test.png