# Inputs
input: # please fill in - example: "path/to/file"
# layer: "foo"
modality: "rna"
# input_obs_batch: "foo"
# input_obs_label: "foo"
# input_var_gene_names: "foo"
# input_obs_size_factor: "foo"

# Reference
reference: # please fill in - example: "path/to/file"
# reference_class: "SCANVI"

# Outputs
# output: "$id.$key.output"
# model_output: "model"
obsm_output: "X_integrated_scanvi"
obs_output_predictions: "scanvi_pred"
obs_output_probabilities: "scanvi_proba"
# output_compression: "gzip"

# Early stopping arguments
# early_stopping: true
early_stopping_monitor: "elbo_validation"
early_stopping_patience: 45
early_stopping_min_delta: 0.0

# Learning parameters
# max_epochs: 123
reduce_lr_on_plateau: true
lr_factor: 0.6
lr_patience: 30.0

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

# Arguments
