@include "rna/_common_cloupe_stages.mro"

call CLOUPE_PREPROCESS(
    pipestance_type              = "SC_RNA_COUNTER_CS",
    sample_id                    = "cellranger-Aiptasia-sym_reprep1",
    sample_desc                  = "Aiptasia-sym_reprep1",
    analysis                     = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u29f8cfd447/files/analysis",
    filtered_gene_bc_matrices_h5 = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/filtered_matrices_h5.h5",
    metrics_json                 = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u29f8cfd517/files/metrics_summary_json.json",
    aggregation_csv              = null,
    gem_group_index_json         = null,
    image_page_names             = null,
    tissue_image_paths           = null,
    dark_images                  = null,
    tissue_positions             = null,
    fiducial_positions_list      = null,
    dzi_info                     = null,
    dzi_tiles_paths              = null,
    scale_factors_json           = null,
    no_secondary_analysis        = false,
    barcode_whitelist            = null,
    hd_slide_name                = null,
    loupe_map                    = null,
    product_type                 = "sc",
    cells_per_sample             = null,
    cells_per_tag                = null,
    cells_per_protospacer        = null,
    spatial_enrichment           = null,
    spatial_deconvolution_path   = null,
    disable_cloupe               = null,
)
