@include "rna/_cr_lib_stages.mro"

call WRITE_H5_MATRIX(
    gem_well          = 1,
    counts            = [
        "/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_sort.csf",
        "/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_sort.csf",
        "/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_sort.csf",
        "/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_sort.csf",
        "/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_sort.csf",
    ],
    bcs               = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ue5873daf42/files/correct_barcode_counts.bcc.bincode",
    barcode_whitelist = "visium-v1",
    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",
    chemistry_def     = {
        "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",
    },
    sample_id         = "399-A1",
)
