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

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

# Neighbour calculation
uns_neighbors: "harmonypy_integration_neighbors"
obsp_neighbor_distances: "harmonypy_integration_distances"
obsp_neighbor_connectivities: "harmonypy_integration_connectivities"

# Harmony integration options
embedding: "X_pca"
obsm_integrated: "X_pca_integrated"
obs_covariates: # please fill in - example: ["batch", "sample"]
theta: [2.0]

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

# Umap options
obsm_umap: "X_leiden_harmony_umap"

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

# Arguments
