How to link a project to a pipeline

One of the advantages of looper is that it decouples projects and pipelines, so you can have many projects that all use the same pipeline, or many pipelines running on the same project. This modular connection between pipelines and projects happens through a file called the pipeline interface. The pipeline interface tells looper how to run the pipeline.

If you're using one or more existing looper-compatible pipelines, all you have to do is point your project config file at the pipeline interface files for any pipelines your project needs. For most casual users of pipelines, that's all you'll need to do; you'll never need to create a new pipeline interface file. But if you do need to make a new pipeline looper-compatible, you do this by creating a pipeline interface file, which is explained in Writing a pipeline interface.

Pointing your PEP to an existing pipeline interface file

Many projects will require only existing pipelines that are already looper-compatible. We maintain a (growing) list of public looper-compatible pipelines that will get you started. To use one of these pipelines, first clone the desired code repository. Then, use the pipeline_interfaces key in the metadata section of a project config file to point your project to that pipeline_interface file:

    pipeline_interfaces: /path/to/cloned/pipeline_interface.yaml

The value for the pipeline_interfaces key should be the absolute path to the pipeline interface file. After that, you just need to make sure your project definition provides all the necessary sample metadata required by the pipeline you want to use. For example, you will need to make sure your sample annotation sheet specifies the correct value under protocol that your linked pipeline understands. Such details are specific to each pipeline and should be defined somewhere in the pipeline's documentation, e.g. in a README file.

You can also link more than one pipeline.