Access the workflow profiles

The profile subcommand provides several commands to manage the workflow profiles. Profiles are used to define different configurations for the workflow e.g. you can configure how the workflow will run on a HPC. You can read more about profiles in the Snakemake documentation.

Note

For snk to be able to access the profiles, the profiles must be located in the profiles directory of the workflow.

List

List the profiles in the workflow.

snk-basic-pipeline profile list

Show

The show command will display the contents of a profile.

snk-basic-pipeline profile show slurm

You can save the profiles by piping the output to a file.

snk-basic-pipeline profile show slurm > profile/config.yaml

Note

You must save the profile as config.yaml in a directory so that it can be accessed by the workflow.

Load a profile

You can load a profile by using the --profile option in the run command.

snk-basic-pipeline run --profile profile/config.yaml

Edit

The edit command will open the profile in the default editor. Changes saved will modify the default profile settings for the installation.

snk-basic-pipeline profile edit slurm