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

# Mitochondrial & Ribosomal Gene Detection
# var_gene_names: "gene_symbol"
# var_name_mitochondrial_genes: "foo"
# obs_name_mitochondrial_fraction: "foo"
mitochondrial_gene_regex: "^[mM][tT]-"
# var_name_ribosomal_genes: "foo"
# obs_name_ribosomal_fraction: "foo"
ribosomal_gene_regex: "^[Mm]?[Rr][Pp][LlSs]"

# QC metrics calculation options
# var_qc_metrics: ["ercc,highly_variable"]
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"

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

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

# Arguments
