pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
20 stars 7 forks source link

Customize looper config via cli #446

Closed donaldcampbelljr closed 5 months ago

donaldcampbelljr commented 5 months ago

Closes #379

Allows configuring looper config via the CLI, e.g.:

looper run -d --looper-dict pep_config=project/project_config.yaml 
output_dir="results" sample_pipeline_interface=pipeline/pipeline_interface.yaml
khoroshevskyi commented 5 months ago

I think this PR should not be merged. I would like to be wrong, If you will have chance, please explain me why this changes needed

donaldcampbelljr commented 5 months ago

This is simply an alternate option. Instead of providing a path to a looper config file, the user can pass the items via CLI.

            subparser.add_argument(
                "--looper-dict",
                required=False,
                default=None,
                type=str,
                nargs="+",
                help="Looper configuration list of key value pairs (k1=v1)",
            )

User can use --looper-config with a path to a looper config file OR use --looper-dict to provide key:value pairs that configure looper.

khoroshevskyi commented 5 months ago

ok, I see..., can we discuss it with everyone before merging ?