@include "rna/_sc_rna_analyzer_stages.mro"

call PREPROCESS_MATRIX(
    matrix_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",
    random_seed               = null,
    use_genes                 = null,
    exclude_genes             = null,
    use_bcs                   = null,
    num_bcs                   = null,
    # NOTE: this is null because the cells are already forced in FILTER_BARCODES
    force_cells               = null,
    get_peak_matrix           = false,
    skip                      = false,
    is_visium_hd              = false,
    is_pd                     = false,
    is_antibody_only          = false,
    disable_run_pca           = false,
    disable_correct_chemistry_batch = true,
    skip_multigenome_analysis = false,
    enable_tsne               = true,
)
