@include "_sc_rna_analyzer_stages.mro"

call ANALYZER_PREFLIGHT(
    skip = true,
    raw_matrices_h5 = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-u40122a12e8/files/matrices_h5.h5",
    filtered_matrices_h5 = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u40122a1c5f/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,
)