@include "rna/_sc_rna_analyzer_stages.mro"

call ANALYZER_PREFLIGHT(
    no_secondary_analysis      = false,
    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",
    use_genes                  = null,
    exclude_genes              = null,
    use_bcs                    = null,
    num_analysis_bcs           = null,
    force_cells                = null,
    random_seed                = 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,
    tsne_max_dims              = null,
    tsne_max_iter              = null,
    tsne_stop_lying_iter       = null,
    tsne_mom_switch_iter       = null,
    tsne_theta                 = null,
    umap_n_neighbors           = null,
    umap_input_pcs             = null,
    umap_max_dims              = null,
    umap_min_dist              = null,
    umap_metric                = null,
    chemistry_batch_correction = false,
    skip_multigenome_analysis  = false,
)
