pepkit / looper

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

the pipeline interface `init` function specifies an output schema, but doesn't initialize one. #418

Closed donaldcampbelljr closed 6 months ago

donaldcampbelljr commented 8 months ago

There are two commands: looper init-piface -> generates a pipeline interface

pipeline_name: count_lines
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}'

Is the desire that the above command would also generate an output_schema.yaml ?

The 2nd command: looper init pep_config -> generates a looper config

  pep_config: pep_path
  output_dir: output_dir
  pipeline_interfaces: 
      sample: sample_pipeline_interface
      project: project_pipeline_interfaces,

However, this command does not involve an output_schema.

Could you clarify the ask, @nsheff ?

donaldcampbelljr commented 8 months ago

would be nice to have an output schema that you could edit and use.

might have value in also spawning the count_lines.sh (as a generic pipeline)