# Inputs
input: # please fill in - example: "path/to/file"
modality: "rna"
# input_layer: "foo"
# var_input: "foo"
# var_gene_names: "foo"
obs_labels: # please fill in - example: "foo"
unlabeled_category: "Unknown"

# scVI Model
scvi_model: # please fill in - example: "scvi_model.pt"

# Outputs
# output: "$id.$key.output"
# output_model: "$id.$key.output_model"
obsm_output: "X_scanvi_integrated"
obs_output_predictions: "scanvi_pred"
obs_output_probabilities: "scanvi_proba"
# output_compression: "gzip"

# scANVI training arguments
# early_stopping: true
early_stopping_monitor: "elbo_validation"
early_stopping_patience: 45
early_stopping_min_delta: 0.0
# 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
