# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: ["input.h5mu"]
# rna_layer: "foo"
# prot_layer: "foo"

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

# Highly variable features detection
highly_variable_features_var_output: "filter_with_hvg"
highly_variable_features_obs_batch_key: "sample_id"

# QC metrics calculation options
var_qc_metrics: ["filter_with_hvg"]
top_n_vars: [50, 100, 200, 500]

# PCA options
pca_overwrite: false

# CLR options
clr_axis: 0

# RNA Scaling options
rna_enable_scaling: false
rna_scaling_output_layer: "scaled"
rna_scaling_pca_obsm_output: "scaled_pca"
rna_scaling_pca_loadings_varm_output: "scaled_pca_loadings"
rna_scaling_pca_variance_uns_output: "scaled_pca_variance"
rna_scaling_umap_obsm_output: "scaled_umap"
# rna_scaling_max_value: 123.0
rna_scaling_zero_center: true

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

# Arguments
