pipeline_interface_simple_test.yaml

pipeline_name: demo
pipeline_type: sample
# input_schema: bwa_input_schema.yaml
pre_submit:
  python_functions:
  - refgenconf.looper_refgenie_populate
  - looper.write_sample_yaml
  - looper.write_custom_template
command_template: >
  echo {project.genome}
var_templates:
  refgenie_config: "$REFGENIE"
  custom_template: in.jinja
  custom_template_output: "{looper.output_dir}/submission/{sample.sample_name}_custom_config.yaml"