# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: "dataset.h5mu"
# layer: "foo"
modality: "rna"

# Outputs
# output: "$id.$key.output.h5mu"
# output_model: "$id.$key.output_model"

# Neighbour calculation
uns_neighbors: "scvi_integration_neighbors"
obsp_neighbor_distances: "scvi_integration_distances"
obsp_neighbor_connectivities: "scvi_integration_connectivities"

# Scvi integration options
obs_batch: # please fill in - example: "foo"
obsm_output: "X_scvi_integrated"
# var_input: "foo"
# 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

# Clustering options
obs_cluster: "scvi_integration_leiden"
leiden_resolution: [1.0]

# Umap options
obsm_umap: "X_scvi_umap"

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

# Arguments
