@include "rna/_sc_rna_analyzer_stages.mro"

call ANALYZER_PREFLIGHT(
    skip                 = false,
    filtered_matrices_h5 = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_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,
)
