@include "rna/sc_rna_analyzer.mro"

call SC_RNA_ANALYZER(
    aggregate_barcodes = null,
    analyzer_inputs    = {
        aggr_library_info:          null,
        cbc_alpha:                  null,
        cbc_knn:                    null,
        cbc_realign_panorama:       null,
        cbc_sigma:                  null,
        chemistry_batch_correction: false,
        enable_tsne:                true,
        exclude_genes:              null,
        filtered_matrices_h5:       "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/filtered_matrices_h5.h5",
        # NOTE: this is null because the cells are already forced in FILTER_BARCODES
        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-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u29f8cfd3d5/files/molecule_info_non_multiplexed.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,
    },
)
