AI-MARRVEL Runner for PhEval

This is the AI-MARRVEL plugin for PhEval. With this plugin, you can leverage the tool, AI-MARRVEL, to run the PhEval pipeline seamlessly. Detailed instructions on setting up the appropriate directory layout, including the input directory and test data directory, can be found here.

Installation

git clone https://github.com/yaseminbridges/pheval.ai_marrvel.git
cd pheval.ai_marrvel
poetry install
poetry shell

Alternative install with pip

pip install pheval-ai-marrvel

Configuring a single run:

Setting up the input directory

A config.yaml should be located in the input directory and formatted like so:

tool: AI-MARRVEL
tool_version: 1.0.0
variant_analysis: True
gene_analysis: True
disease_analysis: False
tool_specific_configuration_options:
  environment: nextflow # either apptainer/docker/nextflow

The AI-MARRVEL data dependencies should also be unpacked into the input directory. The overall structure of the input directory should look something like:

.
├── annotate
├── bcf_annotate 
├── config.yaml
├── filter_vep
├── merge_expand
├── mod5_diffusion
├── model_inputs
├── omim_annotate
├── phrank
├── predict_new 
├── var_tier 
└── vep 

The testdata directory should include the subdirectory named phenopackets - which should contain phenopackets and vcf - which should contain the gzipped VCF files.

e.g.,

├── testdata_dir
   ├── phenopackets
   └── vcf

Run command

pheval run --input-dir /path/to/input_dir \
--runner aimarrvelrunner \
--output-dir /path/to/output_dir \
--testdata-dir /path/to/testdata_dir