TBD: Modular Workflow Execution

  • Running individual modules:
    • Starting from Module 2 if data is already phased.
    • Skipping to specific stages if local ancestry estimates are available.
  • Sequential Execution: Running the workflow one module at a time.

The pipeline is designed into three independent modules:

  1. Module 1: Phasing (using SHAPEIT5)
  2. Module 2: Local Ancestry Inference (using RFMix2, G-Nomix, FLARE)
  3. Module 3: Tractor GWAS

The whole workflow can be run together, as we discussed in Launching an NXF Workflow, but these modules can also be run indepdendently or two at a time.

Here we discuss the scripts to be able to independently run these modules:

This section will soon be updated.