@include "rna/_sc_multi_defs.mro"

call MULTI_REPORTER(
    sample_id                    = "Nodule_1gex_only",
    sample_desc                  = "",
    multi_config_sha             = null,
    config                       = {
        disable_count:       false,
        disable_multi:       true,
        disable_multi_count: true,
        disable_vdj_b:       true,
        disable_vdj_t:       true,
        disable_vdj_t_gd:    true,
        has_no_vdj_ref:      true,
    },
    count_pipestance_type        = "SC_RNA_COUNTER_CS",
    feature_reference            = null,
    reference_path               = "/data/adf/meeting_prep/soy_Williams82_v3_with_organelles",
    count_gw                     = {
        basic_counter_outs: {
            aggregate_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/aggregate_barcodes.csv",
            alignments: [
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
                "/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/pos_sorted.asf",
            ],
            annotation_files:              null,
            assign_tags:                   null,
            bam_header:                    "/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/join-u9474a469ce/files/bam_header",
            barcode_correction_csv:        "/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/join-u9474a469ce/files/barcode_summary.csv",
            barcode_counts:                "/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/BARCODE_CORRECTION/fork0/join-u9474a469c5/files/total_barcode_counts.tbcc.bincode",
            barcode_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/WRITE_BARCODE_SUMMARY/fork0/chnk0-u9474a46b4a/files/barcode_summary.h5",
            bc_umi_info: [
                "/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",
            ],
            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",
            filtered_gene_bc_matrices_h5:  "/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_matrices_h5.h5",
            filtered_gene_bc_matrices_mex: "/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_matrices_mex",
            gem_groups:                    [1],
            gem_well_alignment_metrics:    "/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/COLLATE_METRICS/fork0/chnk0-u9474a46b4a/files/summary.json",
            gem_well_throughput:           null,
            merged_subsampling_metrics:    "/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/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u9474a46be6/files/merged_metrics.pickle",
            molecule_info:                 "/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/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u9474a46bd6/files/molecule_info_non_multiplexed.h5",
            multi_matrices:                null,
            multi_metrics:                 null,
            multi_molecule_info:           null,
            multi_pos_sorted_bam:          null,
            nonambient_cell_calls:         "/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/nonambient_calls.csv",
            per_barcode_metrics:           "/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/COLLATE_METRICS/fork0/chnk0-u9474a46b4a/files/per_barcode_metrics.csv",
            per_barcode_metrics_shard: [
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
                "/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/metrics_shard.bmsf",
            ],
            per_probe_metrics:             null,
            possorted_genome_bai_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/WRITE_POS_BAM/fork0/join-u9474a46b56/files/pos_sorted_non_multiplexed.bam.bai",
            possorted_genome_bam:          "/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/WRITE_POS_BAM/fork0/join-u9474a46b56/files/pos_sorted_non_multiplexed.bam",
            possorted_genome_csi_index:    null,
            raw_gene_bc_matrices_h5:       "/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_H5_MATRIX/fork0/chnk0-u9474a46b4a/files/raw_feature_bc_matrix.h5",
            raw_gene_bc_matrices_mex:      "/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_MATRIX_MARKET/fork0/chnk0-u9474a46b4a/files/raw_feature_bc_matrix",
            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,
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)
