@include "rna/_basic_sc_rna_counter_stages.mro"

call SUMMARIZE_BASIC_REPORTS(
    matrices_h5             = "/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",
    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",
    per_barcode_metrics     = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ue5873db1f5/files/per_barcode_metrics.csv",
    matrix_computer_summary = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ue5873db1f6/files/summary.json",
    barcode_summary         = "/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",
    recovered_cells         = null,
    reference_path          = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    barcode_whitelist       = "visium-v1",
    gem_groups              = [1],
    summary_jsons           = [
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ue5873db1f6/files/summary.json",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-ue5873db278/files/summary.json",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ue5873db265/files/summary.json",
        "/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/summary.json",
    ],
)
