scripts folder#
This folder contains scripts to run various steps of the pipeline from the command line or via snakemake.
scripts.preprocess_test_sample script#
A script that runs the preprocessing of a test sample.
scripts.process_test_sample script#
A script that runs the preprocessing of a test sample.
scripts.train_model script#
A script that runs the training of a model (embedding or GNN).
- scripts.train_model.train_model(path_or_config, step, identifier=None)[source]#
Run the training of a model.
- Parameters:
path_or_config (
str|dict) – pipeline configuration or path to it.step (
str) – Model step, such as embedding or gnn.identifier (
Optional[str]) – Identifier added at the end of the step name.
- Return type:
Tuple[Trainer,Module]- Returns:
Trainer and trained model.