@include "rna/sc_rna_analyzer.mro"

call SC_RNA_ANALYZER(
    aggregate_barcodes = null,
    analyzer_inputs    = {
        aggr_library_info: [
            {
                aggr_id:           "cellranger-Aiptasia-apo_rep1",
                batch_id:          0,
                batch_name:        "cellranger-Aiptasia-apo_rep1",
                gem_group:         1,
                library_id:        0,
                library_type:      "Gene Expression",
                old_gem_group:     1,
                old_library_index: 0,
                target_set_name:   null,
            },
            {
                aggr_id:           "cellranger-Aiptasia-pilot_Apo_Sym",
                batch_id:          1,
                batch_name:        "cellranger-Aiptasia-pilot_Apo_Sym",
                gem_group:         2,
                library_id:        1,
                library_type:      "Gene Expression",
                old_gem_group:     1,
                old_library_index: 0,
                target_set_name:   null,
            },
            {
                aggr_id:           "cellranger-Aiptasia-superloading_Sym",
                batch_id:          2,
                batch_name:        "cellranger-Aiptasia-superloading_Sym",
                gem_group:         3,
                library_id:        2,
                library_type:      "Gene Expression",
                old_gem_group:     1,
                old_library_index: 0,
                target_set_name:   null,
            },
            {
                aggr_id:           "cellranger-Aiptasia-sym_rep1",
                batch_id:          3,
                batch_name:        "cellranger-Aiptasia-sym_rep1",
                gem_group:         4,
                library_id:        3,
                library_type:      "Gene Expression",
                old_gem_group:     1,
                old_library_index: 0,
                target_set_name:   null,
            },
            {
                aggr_id:           "cellranger-Aiptasia-sym_reprep1",
                batch_id:          4,
                batch_name:        "cellranger-Aiptasia-sym_reprep1",
                gem_group:         5,
                library_id:        4,
                library_type:      "Gene Expression",
                old_gem_group:     1,
                old_library_index: 0,
                target_set_name:   null,
            },
        ],
        cbc_alpha:                  null,
        cbc_knn:                    null,
        cbc_realign_panorama:       null,
        cbc_sigma:                  null,
        chemistry_batch_correction: false,
        enable_tsne:                false,
        exclude_genes:              null,
        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",
        force_cells:                null,
        graphclust_neighbors:       null,
        graphclust_resolution:      null,
        is_pd:                      false,
        is_spatial:                 false,
        is_visium_hd:               false,
        max_clusters:               null,
        molecule_info:              "/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",
        neighbor_a:                 null,
        neighbor_b:                 null,
        no_secondary_analysis:      false,
        num_analysis_bcs:           null,
        num_pca_bcs:                null,
        num_pca_genes:              null,
        num_principal_comps:        null,
        random_seed:                null,
        skip_multigenome_analysis:  false,
        tsne_input_pcs:             null,
        tsne_max_dims:              null,
        tsne_max_iter:              null,
        tsne_mom_switch_iter:       null,
        tsne_perplexity:            null,
        tsne_stop_lying_iter:       null,
        tsne_theta:                 null,
        umap_implementation:        "original",
        umap_input_pcs:             null,
        umap_max_dims:              null,
        umap_metric:                null,
        umap_min_dist:              null,
        umap_n_neighbors:           null,
        use_bcs:                    null,
        use_genes:                  null,
    },
)
