@include "sc_rna_analyzer.mro"

call SC_RNA_ANALYZER(
    raw_matrices_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-u85e8945911/files/matrices_h5.h5",
    filtered_matrices_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u85e8948a9f/files/filtered_matrices_h5.h5",
    aggr_library_info = null,
    no_secondary_analysis = false,
    use_genes = null,
    exclude_genes = null,
    use_bcs = null,
    num_analysis_bcs = null,
    random_seed = null,
    num_pca_bcs = null,
    num_pca_genes = null,
    num_principal_comps = null,
    chemistry_batch_correction = false,
    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,
    force_cells = null,
)