@include "rna/_common_cloupe_stages.mro"

call CLOUPE_PREPROCESS(
    pipestance_type              = "SC_RNA_REANALYZER_CS",
    sample_id                    = "dimitri_force_5000",
    sample_desc                  = "",
    analysis                     = "/scratch/etanis/software/cellranger-6.1.2/dimitri_force_5000/SC_RNA_REANALYZER_CS/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-uc0425ec773/files/analysis",
    filtered_gene_bc_matrices_h5 = "/scratch/etanis/software/cellranger-6.1.2/dimitri_force_5000/SC_RNA_REANALYZER_CS/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-uc0425ec74a/files/cloupe_matrix_h5.h5",
    metrics_json                 = null,
    aggregation_csv              = null,
    gem_group_index_json         = null,
    tissue_image_paths           = null,
    dark_images                  = null,
    tissue_positions_list        = null,
    fiducial_positions_list      = null,
    dzi_info                     = null,
    dzi_tiles_paths              = null,
    scale_factors_json           = null,
    no_secondary_analysis        = false,
    barcode_whitelist            = null,
    loupe_map                    = null,
    product_type                 = "sc",
    cells_per_tag                = null,
    cells_per_protospacer        = null,
    spatial_enrichment           = null,
)
