@include "rna/_spatial_reporting_stages.mro"

call SPATIAL_REPORTER(
    summaries               = [
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-ufe8a68034a/files/summary.json",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/summary.json",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/alignment_metrics.json",
        null,
        null,
    ],
    sample_id               = "ST358_A1",
    sample_desc             = "",
    slide_serial_info       = "V12U06-358-A1",
    reference_path          = "/gpfs/data/yanailab/refs/homo_sapiens/hg38_mm10_10X/hg38_and_mm10",
    analysis                = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis",
    barcode_summary_h5      = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ufe8a680090/files/barcode_summary.h5",
    filtered_barcodes       = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_barcodes.csv",
    barcode_whitelist       = "visium-v1",
    gem_groups              = [1],
    matrix                  = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ufe8a680090/files/raw_feature_bc_matrix.h5",
    scalefactors            = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json",
    aligned_fiducials       = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/aligned_fiducials.jpg",
    fraction_under_tissue   = 0.6189903846153846,
    tissue_hires_image      = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/STANDARDIZE_IMAGES/fork0/join-ufe8a67f4d3/files/tissue_hires_image.png",
    tissue_lowres_image     = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/STANDARDIZE_IMAGES/fork0/join-ufe8a67f4d3/files/tissue_lowres_image.png",
    detected_tissue_image   = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/detected_tissue_image.jpg",
    tissue_positions_list   = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv",
    target_set_name         = null,
    per_feature_metrics_csv = null,
)
