@include "rna/_common_cloupe_stages.mro"

call CLOUPE_PREPROCESS(
    pipestance_type              = "SPATIAL_RNA_COUNTER_CS",
    sample_id                    = "399-A1",
    sample_desc                  = "",
    analysis                     = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis",
    filtered_gene_bc_matrices_h5 = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5",
    metrics_json                 = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json",
    aggregation_csv              = null,
    gem_group_index_json         = null,
    tissue_image_paths           = ["/gpfs/home/jw7078/ST-399/ST-399-A1.jpg"],
    dark_images                  = 0,
    tissue_positions_list        = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv",
    fiducial_positions_list      = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt",
    dzi_info                     = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json",
    dzi_tiles_paths              = ["/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files"],
    scale_factors_json           = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json",
    no_secondary_analysis        = false,
    barcode_whitelist            = "visium-v1",
    loupe_map                    = null,
    product_type                 = "sp",
)
