@include "rna/spatial_rna_counter.mro"

call SPATIAL_RNA_COUNTER(
    sample_id                 = "399-A1",
    sample_def                = [
        {
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/gpfs/data/yanailab/runs/2023-04-15",
            "sample_indices": ["any"],
            "sample_names": ["BS21014A"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    slide_serial_capture_area = "V12D12-399-A1",
    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,
        },
    ],
    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",
    },
    barcode_whitelist         = "visium-v1",
    reference_path            = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    recovered_cells           = null,
    force_cells               = null,
    subsample_rate            = null,
    initial_reads             = null,
    sample_desc               = "",
    r1_length                 = null,
    r2_length                 = null,
    trim_polya_min_score      = 20,
    trim_tso_min_score        = 20,
    no_bam                    = false,
    no_secondary_analysis     = false,
    no_target_umi_filter      = true,
    rps_limit                 = null,
    aligner                   = null,
    is_pd                     = false,
    barcodes_under_tissue     = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/barcodes_under_tissue.json",
    fraction_under_tissue     = 0.21394230769230768,
    alignment_metrics         = "/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",
    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",
    tissue_hires_img          = "/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_img         = "/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_img       = "/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",
    image_scale_factors       = "/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",
    feature_reference         = null,
    is_antibody_only          = false,
)
