@include "rna/_cr_lib_stages.mro"

call WRITE_POS_BAM(
    bam_header           = "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/bam_header",
    alignments           = [
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk16-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk17-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk18-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk19-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk20-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk21-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk22-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk23-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk24-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk25-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk26-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk27-u4c9f5eb328/files/pos_sorted.asf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/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/chnk28-u4c9f5eb328/files/pos_sorted.asf",
    ],
    read_chunks          = [
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-august-2016",
                    },
                ],
                "description": "Single Cell 5' R2-only",
                "endedness": "five_prime",
                "name": "SC5P-R2",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "-",
                "umi": {
                    "length": 10,
                    "min_length": null,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 0,
            "fastq_id": null,
            "fastqs": {
                "i1": null,
                "i2": null,
                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_RNA_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_RNA_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "dimitri:0:1:HKLTCBGXL:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-august-2016",
                    },
                ],
                "description": "Single Cell 5' R2-only",
                "endedness": "five_prime",
                "name": "SC5P-R2",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "-",
                "umi": {
                    "length": 10,
                    "min_length": null,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 1,
            "fastq_id": null,
            "fastqs": {
                "i1": null,
                "i2": null,
                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_BCR_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_BCR_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "dimitri:0:1:HKLTCBGXL:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-august-2016",
                    },
                ],
                "description": "Single Cell 5' R2-only",
                "endedness": "five_prime",
                "name": "SC5P-R2",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "-",
                "umi": {
                    "length": 10,
                    "min_length": null,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 2,
            "fastq_id": null,
            "fastqs": {
                "i1": null,
                "i2": null,
                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_TCR_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_TCR_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "dimitri:0:1:HKLTCBGXL:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    target_set_name      = null,
    sample_barcodes_json = null,
    no_bam               = false,
)
