@include "rna/_sc_rna_aggregator_stages.mro"

call NORMALIZE_DEPTH(
    gem_group_index          = {
        "1": [
            "cellranger-Aiptasia-apo_rep1",
            1,
        ],
        "2": [
            "cellranger-Aiptasia-pilot_Apo_Sym",
            1,
        ],
        "3": [
            "cellranger-Aiptasia-superloading_Sym",
            1,
        ],
        "4": [
            "cellranger-Aiptasia-sym_rep1",
            1,
        ],
        "5": [
            "cellranger-Aiptasia-sym_reprep1",
            1,
        ],
    },
    molecules                = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/MERGE_MOLECULES/fork0/join-u78ffd1af93/files/merged_molecules.h5",
    normalization_mode       = "mapped",
    gem_group_barcode_ranges = {
        "1": [
            0,
            388618,
        ],
        "2": [
            388618,
            747953,
        ],
        "3": [
            747953,
            1113631,
        ],
        "4": [
            1113631,
            1694356,
        ],
        "5": [
            1694356,
            2069118,
        ],
    },
    targeted_depth_factor    = 2,
)
