This pipeline serves as a reference implementation for machine learning models build with mlf-core using the mlflow-xgboost template. The herefore trained mlf-core model can be found here together with the corresponding python package.
All predictions performed during pipeline execution are run on the GPU. To facilitate GPU usage you require CUDA and the NVIDIA container toolkit installed.
Build the Docker container using docker build -t nextflow/lcep:1.0.0 ..
Next, run the pipeline via
nextflow run main.nf -with-docker --pathways data/pathways_ensembl_cancer_2021.csv