# Query Input
id: # please fill in - example: "foo"
input: # please fill in - example: "input.h5mu"
modality: "rna"
# layer: "foo"
input_obs_batch_label: # please fill in - example: "sample"
# input_obs_size_factor: "foo"
# input_var_gene_names: "foo"

# Reference input
reference: # please fill in - example: "reference.h5mu"
reference_obs_target: # please fill in - example: "cell_type"
reference_obs_batch_label: # please fill in - example: "sample"
# reference_obs_size_factor: "foo"
unlabeled_category: "Unknown"
# reference_var_hvg: "foo"
# reference_var_gene_names: "foo"

# scVI, scANVI and scArches training options
# 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

# Leiden clustering options
leiden_resolution: [1.0]

# Neighbor classifier arguments
knn_weights: "uniform"
knn_n_neighbors: 15

# Outputs
# output: "$id.$key.output.h5mu"
output_obs_predictions: "scanvi_pred"
output_obs_probability: "scanvi_probabilities"
output_obsm_integrated: "X_integrated_scanvi"
# output_compression: "gzip"
# output_model: "$id.$key.output_model"

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

# Arguments
