@include "rna/_cr_lib_stages.mro"

call WRITE_MOLECULE_INFO(
    gem_well                  = 1,
    counts_bc_order           = [
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9474a469ce/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9474a469ce/files/bc_umi_info.bui",
    ],
    reference_path            = "/data/adf/meeting_prep/soy_Williams82_v3_with_organelles",
    read_chunks               = [
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": {
                            "name": "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",
                        "whitelist": null,
                    },
                ],
            },
            "chunk_id": 0,
            "fastq_id": null,
            "fastqs": {
                "i1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S2_L004_I1_001.fastq.gz",
                "i2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S2_L004_I2_001.fastq.gz",
                "r1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S2_L004_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S2_L004_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "Nodule_1gex_only:0:1:HWLTCDSX3:4",
            "read_lengths": {},
            "subsample_rate": null,
            "umi_extractor": {
                "translators": [null],
            },
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": {
                            "name": "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",
                        "whitelist": null,
                    },
                ],
            },
            "chunk_id": 1,
            "fastq_id": null,
            "fastqs": {
                "i1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L001_I1_001.fastq.gz",
                "i2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L001_I2_001.fastq.gz",
                "r1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "Nodule_1gex_only:0:1:HCTGKDRX2:1",
            "read_lengths": {},
            "subsample_rate": null,
            "umi_extractor": {
                "translators": [null],
            },
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": {
                            "name": "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",
                        "whitelist": null,
                    },
                ],
            },
            "chunk_id": 2,
            "fastq_id": null,
            "fastqs": {
                "i1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L002_I1_001.fastq.gz",
                "i2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L002_I2_001.fastq.gz",
                "r1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule1/RNA/Nodule_1_S4_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "Nodule_1gex_only:0:1:HCTGKDRX2:2",
            "read_lengths": {},
            "subsample_rate": null,
            "umi_extractor": {
                "translators": [null],
            },
        },
    ],
    feature_reference         = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9474a46535/files/feature_reference.frf.bincode",
    filtered_barcodes         = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u9474a46b55/files/filtered_barcodes.csv",
    target_panel_summary      = null,
    matrix_computer_summary   = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u9474a46b50/files/summary.json",
    recovered_cells           = {
        per_gem_well: null,
        per_sample:   null,
    },
    force_cells               = {
        per_gem_well: null,
        per_sample:   null,
    },
    include_introns           = true,
    filter_probes             = null,
    multi_config_sha          = null,
    sample_barcodes           = null,
    per_sample_metrics        = null,
    barcode_index             = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9474a469ce/files/barcode_index.bi.bincode",
    slide_serial_capture_area = null,
)
