@include "rna/_cr_lib_stages.mro"

call ALIGN_AND_COUNT(
    gem_well                    = 1,
    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/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L003_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L003_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L003_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L003_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "pbmc_granulocyte_sorted_10k:0:1:HGWCKDSXY: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": 1,
            "fastq_id": null,
            "fastqs": {
                "i1": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L004_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L004_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L004_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex/pbmc_granulocyte_sorted_10k_S1_L004_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "pbmc_granulocyte_sorted_10k:0:1:HGWCKDSXY:4",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    reference_path              = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    read_shards                 = {
        corrected_reads: [
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3b7f6e869a/files/valid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3b7f6e869a/files/valid_shard.shard",
        ],
        invalid_reads: [
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3b7f6e869a/files/invalid_shard.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3b7f6e869a/files/invalid_shard.shard",
        ],
        valid_reads: [
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3b7f6e6069/files/valid.shard",
            "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk1-u3b7f6e6069/files/valid.shard",
        ],
    },
    feature_counts              = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3b7f6e6062/files/feature_counts.fbc.bincode",
    feature_reference           = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3b7f6e6062/files/feature_reference.frf.bincode",
    target_set                  = null,
    chemistry_def               = {
        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",
        },
    },
    aligner                     = null,
    aligner_subsample_rate      = null,
    include_introns             = true,
    is_pd                       = true,
    # Inputs copied crom _cr_lib_stages. Cleaner way to do this?
    targeted_umi_min_read_count = null,
    transcriptome_min_score     = 30,
    trim_polya_min_score        = 20,
    trim_tso_min_score          = 20,
    total_barcode_counts        = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3b7f6e8699/files/total_barcode_counts.tbcc.bincode",
    barcode_subset              = null,
)
