@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-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/WRITE_MATRICES/fork0/join-u78ffd1afdc/files/filtered_matrix_h5.h5",
    random_seed               = null,
    use_genes                 = null,
    exclude_genes             = null,
    use_bcs                   = null,
    num_bcs                   = null,
    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               = false,
)
