@include "rna/_cr_lib_stages.mro"

call WRITE_MOLECULE_INFO(
    gem_well                = 1,
    counts_bc_order         = [
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk0-ue5873daf48/files/bc_umi_info.bui",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk1-ue5873daf48/files/bc_umi_info.bui",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk2-ue5873daf48/files/bc_umi_info.bui",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk3-ue5873daf48/files/bc_umi_info.bui",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk4-ue5873daf48/files/bc_umi_info.bui",
    ],
    reference_path          = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    read_chunks             = [
        {
            "chemistry": {
                "barcode_read_length": 16,
                "barcode_read_offset": 0,
                "barcode_read_type": "R1",
                "barcode_whitelist": "visium-v1",
                "description": "Spatial 3' v1",
                "endedness": "three_prime",
                "name": "SPATIAL3Pv1",
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2",
                },
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "RA",
                    "R2": null,
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "rna_read2_type": null,
                "rna_read_length": null,
                "rna_read_offset": 0,
                "rna_read_type": "R2",
                "si_read_length": null,
                "si_read_offset": 0,
                "si_read_type": "I1",
                "strandedness": "+",
                "umi_min_read_length": 10,
                "umi_read_length": 12,
                "umi_read_offset": 16,
                "umi_read_type": "R1",
            },
            "chunk_id": 0,
            "fastqs": {
                "i1": null,
                "i2": null,
                "r1": "/gpfs/data/yanailab/runs/2023-04-15/Sample_BS21014A/BS21014A_S5_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/yanailab/runs/2023-04-15/Sample_BS21014A/BS21014A_S5_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "399-A1:0:1:H5GJGBGXT:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    feature_reference       = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ue5873dae13/files/feature_reference.frf.bincode",
    barcode_whitelist       = "visium-v1",
    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",
    target_panel_summary    = null,
    target_set_name         = null,
    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",
    recovered_cells         = null,
    force_cells             = null,
    include_introns         = false,
    multi_config_sha        = null,
)
