@include "rna/_cr_lib_stages.mro"

call WRITE_POS_BAM(
    bam_header           = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-ud1886f8d26/files/bam_header",
    alignments           = [
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-ud1886f8d28/files/pos_sorted.asf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-ud1886f8d28/files/pos_sorted.asf",
    ],
    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/human_brain_3k/gex/human_brain_3k_S1_L001_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L001_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY:1",
            "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/human_brain_3k/gex/human_brain_3k_S1_L002_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L002_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY:2",
            "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": 2,
            "fastq_id": null,
            "fastqs": {
                "i1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L003_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY: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": 3,
            "fastq_id": null,
            "fastqs": {
                "i1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_I1_001.fastq.gz",
                "i2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_I2_001.fastq.gz",
                "r1": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/net/bmc-lab5/data/kellis/users/benjames/seq/human_brain_3k/gex/human_brain_3k_S1_L004_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "human_brain_3k:0:1:HGTYWDSXY:4",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    target_set_name      = null,
    sample_barcodes_json = null,
    no_bam               = false,
)
