@include "rna/_basic_sc_rna_counter_stages.mro"

call FILTER_BARCODES(
    sample_id              = "399-A1",
    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",
    barcode_correction_csv = "/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/join-ue5873daf47/files/barcode_summary.csv",
    is_antibody_only       = false,
    reference_path         = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    gem_groups             = [1],
    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",
    },
    config                 = {
        cell_barcodes:          "/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",
        force_cells:            null,
        override_library_types: null,
        override_mode:          null,
        recovered_cells:        null,
    },
)
