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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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dynamic_variables_command_template needs a relative key #276

Closed nsheff closed 3 years ago

nsheff commented 4 years ago

If I want to include a python script in dynamic_variables_command_template, right now I have to either hard code the path in the pipeline interface, or execute looper from within a particular folder where that script exists.

Instead, this should operate the same with the command_template does, with some key specifying a path that's relative to the pipeline interface file.

stolarczyk commented 4 years ago

works this way:

pipeline_name: refgenie
pipeline_type: sample
input_schema: refgenie_build.yaml
compute:
  dynamic_variables_script_path: build-compute-params.py # path, absolute or relative to the pipeline interface file
  dynamic_variables_command_template: >
    {pipeline.compute.dynamic_variables_script_path} -a {sample.asset}
...