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

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

# Filtering highly variable features
highly_variable_features_var_output: "filter_with_hvg"
highly_variable_features_obs_batch_key: "sample_id"
highly_variable_features_flavor: "seurat"
# highly_variable_features_n_top_features: 123

# QC metrics calculation options
var_qc_metrics: ["filter_with_hvg"]
top_n_vars: [50, 100, 200, 500]
output_obs_num_nonzero_vars: "num_nonzero_vars"
output_obs_total_counts_vars: "total_counts"
output_var_num_nonzero_obs: "num_nonzero_obs"
output_var_total_counts_obs: "total_counts"
output_var_obs_mean: "obs_mean"
output_var_pct_dropout: "pct_dropout"

# RNA Scaling options
enable_scaling: false
scaling_output_layer: "scaled"
# scaling_max_value: 123.0
scaling_zero_center: true

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

# Arguments
