# Inputs
input: # please fill in - example: "path/to/file"
modality: "rna"
# input_layer: "foo"
obs_batch: "sample_id"
# var_gene_names: "foo"
# var_input: "foo"
# obs_labels: "foo"
# obs_size_factor: "foo"
# obs_categorical_covariate: ["foo"]
# obs_continuous_covariate: ["foo"]

# Outputs
# output: "$id.$key.output"
# output_model: "$id.$key.output_model"
obsm_output: "X_scvi_integrated"
# output_compression: "gzip"

# SCVI options
n_hidden_nodes: 128
n_dimensions_latent_space: 30
n_hidden_layers: 2
dropout_rate: 0.1
dispersion: "gene"
gene_likelihood: "nb"

# Variational auto-encoder model options
use_layer_normalization: "both"
use_batch_normalization: "none"
encode_covariates: true
deeply_inject_covariates: false
use_observed_lib_size: false

# 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

# Data validition
n_obs_min_count: 0
n_var_min_count: 0

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

# Arguments
