@include "rna/_cr_lib_stages.mro"

call MAKE_SHARD(
    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",
        },
    },
    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,
        },
    ],
    r1_length              = null,
    r2_length              = null,
    subsample_rate         = 1,
    initial_read_pairs     = null,
    reference_path         = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    feature_reference_path = null,
    target_features        = null,
    target_set             = null,
    target_set_name        = null,
    libraries_to_translate = [],
    write_bc_counts_json   = true,
)
