@include "rna/_spatial_reporting_stages.mro"

call SPATIAL_REPORTER(
    summaries               = [
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-ue5873db2ca/files/summary.json",
        "/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/summary.json",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/alignment_metrics.json",
        null,
        null,
    ],
    sample_id               = "399-A1",
    sample_desc             = "",
    slide_serial_info       = "V12D12-399-A1",
    reference_path          = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    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",
    barcode_summary_h5      = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ue5873db1f5/files/barcode_summary.h5",
    filtered_barcodes       = "/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_barcodes.csv",
    barcode_whitelist       = "visium-v1",
    gem_groups              = [1],
    matrix                  = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ue5873db1f5/files/raw_feature_bc_matrix.h5",
    scalefactors            = "/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",
    aligned_fiducials       = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/aligned_fiducials.jpg",
    fraction_under_tissue   = 0.21394230769230768,
    tissue_hires_image      = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/STANDARDIZE_IMAGES/fork0/join-ue5873dadfe/files/tissue_hires_image.png",
    tissue_lowres_image     = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/STANDARDIZE_IMAGES/fork0/join-ue5873dadfe/files/tissue_lowres_image.png",
    detected_tissue_image   = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/detected_tissue_image.jpg",
    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",
    target_set_name         = null,
    per_feature_metrics_csv = null,
)
