# Input
id: # please fill in - example: "foo"
input: # please fill in - example: "dataset.h5mu"
# layer: "foo"

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

# Filtering options
# min_counts: 200
# max_counts: 5000000
# min_genes_per_cell: 200
# max_genes_per_cell: 1500000
# min_cells_per_gene: 3
# min_fraction_mito: 0.0
# max_fraction_mito: 0.2
# min_fraction_ribo: 0.0
# max_fraction_ribo: 0.2
skip_scrublet_doublet_detection: false

# 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]"

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

# Arguments
