@include "rna/_slfe_cells_reporter.mro"

call _SLFE_CELLS_REPORTER as _CELLS_REPORTER(
    reference_path            = "/data/adf/meeting_prep/soy_Williams82_v3_with_organelles",
    recovered_cells           = {
        per_gem_well: null,
        per_sample:   null,
    },
    force_cells               = {
        per_gem_well: null,
        per_sample:   null,
    },
    slfe_feature_reference    = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a46d48/files/feature_reference.frf.bincode",
    target_panel_summary      = null,
    matrices_h5               = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ua092a4738b/files/raw_feature_bc_matrix.h5",
    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/Nodule_2/RNA/Nodule_2_S5_L001_I1_001.fastq.gz",
                "i2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L001_I2_001.fastq.gz",
                "r1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "Nodule_2_gex_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": 1,
            "fastq_id": null,
            "fastqs": {
                "i1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L002_I1_001.fastq.gz",
                "i2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L002_I2_001.fastq.gz",
                "r1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "Nodule_2_gex_only:0:1:HCTGKDRX2:2",
            "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/Nodule_2/RNA/Nodule_2_S5_L004_I1_001.fastq.gz",
                "i2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L004_I2_001.fastq.gz",
                "r1": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L004_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA/Nodule_2_S5_L004_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "Nodule_2_gex_only:0:1:HWLTCDSX3:4",
            "read_lengths": {},
            "subsample_rate": null,
            "umi_extractor": {
                "translators": [null],
            },
        },
    ],
    gem_well                  = 1,
    report_mol_inputs         = [
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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/chnk14-ua092a47231/files/bc_umi_info.bui",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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/chnk15-ua092a47231/files/bc_umi_info.bui",
    ],
    matrix_computer_summary   = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47391/files/summary.json",
    barcode_summary           = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ua092a4738b/files/barcode_summary.h5",
    filtered_barcodes         = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ua092a4739d/files/filtered_barcodes.csv",
    filter_barcodes_summary   = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ua092a4739d/files/summary.json",
    per_barcode_metrics       = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ua092a4738b/files/per_barcode_metrics.csv",
    include_introns           = true,
    filter_probes             = null,
    multi_config_sha          = null,
    barcode_index             = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_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-ua092a47231/files/barcode_index.bi.bincode",
    slide_serial_capture_area = null,
)
