@include "rna/_sc_rna_aggregator_stages.mro"

call WRITE_MATRICES(
    sample_defs          = [
        {
            "library_id": "cellranger-Aiptasia-apo_rep1",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-pilot_Apo_Sym",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-pilot_Apo_Sym/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-superloading_Sym",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-superloading_Sym/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-sym_rep1",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_rep1/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-sym_reprep1",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/outs/molecule_info.h5",
        },
    ],
    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",
    raw_matrices_h5      = ["/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/NORMALIZE_DEPTH/fork0/chnk0-u78ffd1afb8/files/raw_matrix_h5.h5"],
    raw_nnz              = 35013399,
    filtered_matrices_h5 = ["/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/NORMALIZE_DEPTH/fork0/chnk0-u78ffd1afb8/files/filtered_matrix_h5.h5"],
    filtered_nnz         = 10662877,
    summary              = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/NORMALIZE_DEPTH/fork0/join-u78ffd1afb6/files/summary.json",
    is_pd                = false,
)
