@include "rna/_sc_rna_analyzer_stages.mro"

call RUN_TSNE(
    matrix_h5        = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-ue5873db267/files/preprocessed_matrix_h5.h5",
    pca_h5           = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/CHOOSE_DIMENSION_REDUCTION_OUTPUT/fork0/chnk0-ue5873db279/files/pca_h5.h5",
    skip             = false,
    random_seed      = null,
    perplexity       = null,
    input_pcs        = null,
    max_dims         = null,
    max_iter         = null,
    stop_lying_iter  = null,
    mom_switch_iter  = null,
    theta            = null,
    is_antibody_only = false,
)
