Quickstart

Minimal validation flow

Start from the bundled minimal config:

trait2gene validate src/trait2gene/data/examples/config.minimal.yaml
trait2gene fetch-resources src/trait2gene/data/examples/config.minimal.yaml

Full-run templates

For real runs, start from one of these templates:

  • src/trait2gene/data/examples/config.realpaths.template.yaml

  • src/trait2gene/data/examples/config.precomputed.template.yaml

The most common execution flow is:

trait2gene validate config.yaml
trait2gene doctor --config config.yaml
trait2gene run config.yaml

Standard pipeline order

trait2gene run executes stages in this order:

  1. validate

  2. prepare

  3. magma

  4. feature_prep

  5. pops

  6. prioritize

  7. report

If the config uses a custom y_path, or precomputed MAGMA outputs, the stage plan adjusts automatically to skip unnecessary work while keeping output layout and reporting consistent.

Public example

To reproduce the bundled real-data tutorial:

python scripts/run_public_schizophrenia_example.py