Error in parsing KeyValue pairs from profile · Issue #1186 · snakemake/snakemake (original) (raw)

Snakemake version

v6.9

Describe the bug

We would like to use the default resources in a cluster profile. However, many logical writings lead to errors.

Minimal example

Option 1

Worked prior to snakemake 6 for shure

default_resources:
  - mem_mb=10
  - time=300

is transformed to --default_resources=mem_mb=10 --default_resources=time=300

Option 2

default_resources: "mem_mb=10 time=300"

is transformed to --default_resources=mem_mb=10 time=300

Option 3

This is the most adapted to yaml format

default_resources:
  mem_mb: 10
  time:300

is transformed to --default_resources={ mem_mb=10, time=300 }

Ideally, the option 3 should be parsed correctly to the expected behavior --default_resources mem_mb=10 time=300

Additional context

This is also relevant for other CLI arguments with key=value paris e.g. config