Rendered pipeline interface var_templates need to be passed back to pipeline namespace

This issue was originally discovered during investigation of issue : https://github.com/pepkit/looper/issues/322.

When using var_templates in a pipeline interface yaml file, the command template is rendered and looks to the pipeline namespace. However, the rendered var_templates are only updated in pl_iface NOT the pipeline namespace. This leads to an unresolved path, i.e. could not find the script located at {looper.piface_dir}/count_lines.sh

pipeline_type: sample
output_schema: output_schema.yaml
var_templates:
  pipeline: '{looper.piface_dir}/count_lines.sh'
command_template: >
  {pipeline.var_templates.pipeline} {sample.file} --output-parent `{looper.sample_output_folder}

Solution: update the pipeline interface with the rendred

This issue is now fixed in commit: https://github.com/pepkit/looper/commit/db5a2a7fa5d455eb5c515b452fcf5c040e416438

pepkit / looper

Rendered pipeline interface var_templates need to be passed back to pipeline namespace #356