Looper configuration file

The .looper.yaml file configures looper for your project. It specifies where to find your samples, pipelines, and how to run them.

Basic example

pep_config: ./project_config.yaml
output_dir: ./results
pipeline_interfaces:
  - ./pipeline/pipeline_interface.yaml

Complete reference

Required settings

Key	Type	Description
`pep_config`	string	Path to PEP config file (YAML or CSV) or PEPhub registry path
`output_dir`	string	Directory for pipeline outputs
`pipeline_interfaces`	list	Paths to pipeline interface YAML files

Pipestat configuration

The pipestat section configures result reporting. All keys are optional.

pipestat:
  project_name: my_project
  results_file_path: results.yaml
  flag_file_dir: results/flags

Key	Type	Description
`project_name`	string	Project name for results tracking
`results_file_path`	string	Path to YAML file for storing results
`flag_file_dir`	string	Directory for status flag files
`pephub_path`	string	PEPhub registry path for results storage

Database backends

For PostgreSQL, use a nested database section:

pipestat:
  project_name: my_project
  database:
    dialect: postgresql
    driver: psycopg2
    name: pipestat-db
    user: postgres
    password: ${POSTGRES_PASSWORD}
    host: 127.0.0.1
    port: 5432

Environment variables can be used anywhere in the config with ${VAR} syntax. This is recommended for sensitive values like passwords.

For PEPhub:

pipestat:
  pephub_path: "databio/myproject:results"

PEP config sources

The pep_config value can be:

Local YAML file: ./project_config.yaml
Local CSV file: ./samples.csv (simple projects)
PEPhub registry path: databio/myproject:default

Examples

Minimal configuration

pep_config: samples.csv
output_dir: results
pipeline_interfaces:
  - pipeline_interface.yaml

With pipestat (file backend)

pep_config: ./metadata/project_config.yaml
output_dir: ./results
pipeline_interfaces:
  - ./pipeline/pipeline_interface.yaml
pipestat:
  project_name: my_project
  results_file_path: results.yaml
  flag_file_dir: results/flags

From PEPhub

pep_config: databio/example_project:default
output_dir: ./results
pipeline_interfaces:
  - ./pipeline/pipeline_interface.yaml

Environment variables

You can use environment variables anywhere in the config file with ${VAR} syntax. This is useful for:

Keeping secrets out of config files (database passwords, API keys)
Making configs portable across machines (paths, hostnames)

pipestat:
  database:
    password: ${DB_PASSWORD}
    host: ${DB_HOST}

Looper environment variables

DIVCFG - Path to divvy configuration file (for compute settings)