@include "rna/_sc_rna_aggregator_stages.mro"

call SUMMARIZE_AGGREGATED_REPORTS(
    sample_id                = "cellranger-aggr-Aiptasia",
    sample_desc              = "aggr-Aiptasia",
    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,
        ],
    },
    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/WRITE_MATRICES/fork0/join-u78ffd1afdc/files/filtered_matrix_h5.h5",
    analysis                 = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u78ffd1b0d4/files/analysis",
    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",
        },
    ],
    normalize_depth_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/WRITE_MATRICES/fork0/join-u78ffd1afdc/files/summary.json",
    analyze_matrices_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/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u78ffd1b0d4/files/summary.json",
    antibody_histograms      = null,
    antibody_treemap         = null,
    crispr_analysis_metrics  = null,
    product_type             = "sc",
    skip_tsne                = true,
)
