A project with multiple pipelines

In earlier versions of looper (v < 1.0), we used a protocol_mappings section to map samples with different protocol attributes to different pipelines. In the current pipeline interface (looper v > 1.0), we eliminated the protocol_mappings, because this can now be handled using sample modifiers, simplifying the pipeline interface. Now, each pipeline has exactly 1 pipeline interface. You link to the pipeline interface with a sample attribute. If you want the same pipeline to run on all samples, it's as easy as using an append modifier like this:

sample_modifiers:
  append:
    pipeline_interfaces: "test.yaml"

But if you want to submit different sampels to different pipelines, depending on a sample attribute, like protocol, you can use an implied attribute:

sample_modifiers:
  imply:
    - if:
        protocol: [PRO-seq, pro-seq, GRO-seq, gro-seq] # OR
      then:
        pipeline_interfaces: ["peppro.yaml"]

This approach uses only functionality of PEPs to handle the connection to pipelines as sample attributes, which provides full control and power using the familiar sample modifiers. It completely eliminates the need for re-inventing this complexity within looper, which eliminated the protocol mapping section to simplify the looper pipeline interface files. You can read more about the rationale of this change in issue 244.