reference-update

Automatically build a reference directory structure for a VEuPathDB group for use in Companion pipeline.

Quick Start

1. Ensure Dependencies are installed.
2. Create a params_default.config from the template params_default.example and fill out.
3. Run the following on command line (see Nextflow docs for OPTIONS):

nextflow run reference_update.nf [OPTIONS]

1. If successful, fully populated reference directory will be available at params.REFERENCE_PATH.

Dependencies

• AUGUSTUS
• Companion
• EuPathWS
• OrthoFinder
  • Python 3
  • SciPy