Show the Workflow Configuration

The config subcommand will display the workflow configuration file contents. You can use the --pretty (-p) flag to display the configuration in a more readable format.

snk-basic-pipeline config

genome: data/genome.fa
samples_dir: data/samples
sample:
- A
- B
- C

You can pipe the output to a file to save the configuration.

snk-basic-pipeline config > config.yaml

You can then edit the configuration file and use it to run the workflow.

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