@include "rna/_common_cloupe_stages.mro"

call CLOUPE_PREPROCESS(
    pipestance_type              = "SC_RNA_AGGREGATOR_CS",
    sample_id                    = "cellranger-aggr-Aiptasia",
    sample_desc                  = "aggr-Aiptasia",
    analysis                     = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u78ffd1b0d4/files/analysis",
    filtered_gene_bc_matrices_h5 = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/WRITE_MATRICES/fork0/join-u78ffd1afdc/files/filtered_matrix_h5.h5",
    metrics_json                 = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SUMMARIZE_AGGREGATED_REPORTS/fork0/join-u78ffd1b0d7/files/summary.json",
    aggregation_csv              = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia.csv",
    gem_group_index_json         = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SETUP_SAMPLES/fork0/chnk0-u78ffd1af92/files/gem_group_index_json.json",
    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,
)
