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

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

# Sample ID options
add_id_to_obs: true
add_id_obs_output: "sample_id"
add_id_make_observation_keys_unique: true

# RNA filtering options
# rna_min_counts: 200
# rna_max_counts: 5000000
# rna_min_genes_per_cell: 200
# rna_max_genes_per_cell: 1500000
# rna_min_cells_per_gene: 3
# rna_min_fraction_mito: 0.0
# rna_max_fraction_mito: 0.2
# rna_min_fraction_ribo: 0.0
# rna_max_fraction_ribo: 0.2
skip_scrublet_doublet_detection: false

# CITE-seq filtering options
# prot_min_counts: 3
# prot_max_counts: 5000000
# prot_min_proteins_per_cell: 200
# prot_max_proteins_per_cell: 100000000
# prot_min_cells_per_protein: 3

# GDO filtering options
# gdo_min_counts: 3
# gdo_max_counts: 5000000
# gdo_min_guides_per_cell: 200
# gdo_max_guides_per_cell: 100000000
# gdo_min_cells_per_guide: 3

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

# 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]

# 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
