@include "rna/_cr_lib_stages.mro"

call WRITE_MOLECULE_INFO(
    gem_well                = 1,
    counts_bc_order         = [
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-ud1886f8d28/files/bc_umi_info.bui",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-ud1886f8d28/files/bc_umi_info.bui",
    ],
    reference_path          = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    read_chunks             = [
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-arc-v1",
                    },
                ],
                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                "endedness": "three_prime",
                "name": "ARC-v1",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 0,
            "fastq_id": null,
            "fastqs": {
                "i1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L001_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L001_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-arc-v1",
                    },
                ],
                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                "endedness": "three_prime",
                "name": "ARC-v1",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 1,
            "fastq_id": null,
            "fastqs": {
                "i1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L002_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L002_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY:2",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-arc-v1",
                    },
                ],
                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                "endedness": "three_prime",
                "name": "ARC-v1",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 2,
            "fastq_id": null,
            "fastqs": {
                "i1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY:3",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-arc-v1",
                    },
                ],
                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                "endedness": "three_prime",
                "name": "ARC-v1",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 3,
            "fastq_id": null,
            "fastqs": {
                "i1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY:4",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    feature_reference       = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud1886f6d8a/files/feature_reference.frf.bincode",
    filtered_barcodes       = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud1886fac26/files/cell_barcodes.csv",
    target_panel_summary    = null,
    target_set_name         = null,
    matrix_computer_summary = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ud1886fa2ac/files/summary.json",
    recovered_cells         = 1000,
    force_cells             = null,
    include_introns         = true,
    multi_config_sha        = null,
    sample_barcodes_json    = null,
    per_sample_metrics      = null,
    barcode_index           = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud1886f8d25/files/barcode_index.bi.bincode",
)
