New way to handle the old pipeline_args utility

it used to be you could add this in to the project config:

  pipeline_args:
    rrbs:
      '--epilog': ""
      '--dirty': ""

and then for the rrbs pipeline, these arguments would be automatically added to the pipeline command call created by looper. This is no longer possible because the pipeline_args keyword is no more.

From @stolarczyk:

The problem emerges when I have 1 PEP pointing to multiple pipelines (one to many). And that’s right, since we point to files, not pipeline identifiers, there’s no way to refer to a pipeline unless we pass a tuple as a pipeline interface with the file path and arguments to be appended. Is that worth the effort? Not sure..

2 subprojects within one PEP, or, even more relevant: 1 PEP with 2 pipeline interfaces.

I have not thought of a solution.

pepkit / looper

New way to handle the old pipeline_args utility #256