@include "rna/_cr_lib_stages.mro"

call WRITE_POS_BAM(
    bam_header                = "/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/join-ua092a47231/files/bam_header",
    alignments                = [
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
        "/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/pos_sorted.asf",
    ],
    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],
            },
        },
    ],
    target_set_name           = null,
    sample_barcodes           = null,
    slide_serial_capture_area = null,
)
