@include "rna/sc_rna_aggregator.mro"

call SC_RNA_AGGREGATOR(
    sample_id                = "cellranger-aggr-Aiptasia",
    sample_desc              = "aggr-Aiptasia",
    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",
        },
    ],
    normalization_mode       = "mapped",
    no_secondary_analysis    = false,
    num_analysis_bcs         = null,
    num_pca_bcs              = null,
    num_pca_genes            = null,
    num_principal_comps      = null,
    cbc_knn                  = null,
    cbc_alpha                = null,
    cbc_sigma                = null,
    cbc_realign_panorama     = null,
    max_clusters             = null,
    graphclust_neighbors     = null,
    neighbor_a               = null,
    neighbor_b               = null,
    tsne_perplexity          = null,
    tsne_input_pcs           = null,
    random_seed              = null,
    tsne_max_dims            = null,
    tsne_max_iter            = null,
    tsne_stop_lying_iter     = null,
    tsne_mom_switch_iter     = null,
    tsne_theta               = null,
    product_type             = "sc",
    is_pd                    = false,
    min_crispr_umi_threshold = 3,
    enable_tsne              = false,
)
