How to use the looper config file

Starting with looper version >=1.5.0, you should specify a pipeline interface in the looper config file, rather than in the PEP.

Example looper config file using local PEP:

pep_config: $HOME/hello_looper-master/project/project_config.yaml
output_dir: "$HOME/hello_looper-master/output"
pipeline_interfaces:
  sample: ["$HOME/hello_looper-master/pipeline/pipeline_interface"]
  project: "some/project/pipeline"

In addition, looper>=1.5.0 supports projects from PEPhub. Using a PEP from PEPhub allows a user to run a pipeline without downloading the PEP. This allows you to keep the sample table in a centralized, shared location. You need only specify all necessary environment variables used by the PEP.

Example looper config file using PEPhub project:

pep_config: pephub::databio/looper:default
output_dir: "$HOME/hello_looper-master/output"
pipeline_interfaces:
  sample: ["$HOME/hello_looper-master/pipeline/pipeline_interface"]
  project: "$HOME/hello_looper-master/project/pipeline"

Where: - output_dir is pipeline output directory, where results will be saved. - pep_config is a local config file or PEPhub registry path. (registry path should be specified in one one of supported ways: namespace/name, pephub::namespace/name, namespace/name:tag, or pephub::namespace/name:tag) - pipeline interfaces is a local path to project or sample pipelines.

To run pipeline, go to the directory of .looper.config and execute command in your terminal: looper run --looper-config {looper_config_path} or looper runp --looper-config {looper_config_path}.