How to define key=var arguments in a snakemake profile yaml file

Question

Some of the snakemake arguments follow the key=value pattern. I would like to add them to the snakemake profile yaml file.

for example, the command line arguments should be stored in the snakemake profile.

--default-resources mem=50 time=5

I tried the two following options but it didn't work:

default-resources: "mem=50 time=5"

default-resources: 
  mem: 50
  time: 5

Problem continues for snakemake > 6.3 https://github.com/snakemake/snakemake/issues/1186

Answer 1

I haven't tested this, but since I believe it is a yaml file, I guess you should add a dash per line:

default-resources: 
  - mem: 50
  - time: 5

Answer 2

What worked for me is the following syntax which is a bit at odds with the yaml definition.

default-resources: 
  - mem=50
  - time=5

Where the resources definitions are interpreted as strings.