Configuring new pipelines


A pipeline describes the way in which samples may be processed in lab to produce a library. While processing samples through a pipeline, the users can be expected to create multiple pieces of labware (eg. plates, tubes), and transfer samples between these. Each labware has a particular 'purpose' which established how it behaves, and is displayed to the user. Multiple purposes are linked together to establish the pipeline.

While Limber offers the flexibility to deviate from the prescribed pipelines, the configuration here determines the recommended route through the process, and the one followed in the vast majority of cases.

A pipeline is configured in three main locations:

  1. config/purposes/*.yml
  2. config/pipelines/*.yml
  3. And in the limber.rake task in Sequencescape


Describes each purpose in the pipeline, and how it behaves. purposes_yaml_files


Describes how the purposes link together, and how you know which pipeline you are following. pipelines_yaml_files


Limber processes requests created in Sequencescape when the SSR makes a submission. These requests identify what work is requested through a combination of request_type and library_type, and also specify other customer requested variables, such as primer_panels or bait libraries.

The limber.rake task defines the request types and library types, and helps set up the submission templates that the SSRs will use to generate the submissions.