@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": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "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": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S1_L001_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "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": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S1_L002_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S1_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S1_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:2",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "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": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S2_L001_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S2_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S2_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "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": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S2_L002_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S2_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S2_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:2",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 4,
            "fastq_id": null,
            "fastqs": {
                "i1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S3_L001_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S3_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S3_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 5,
            "fastq_id": null,
            "fastqs": {
                "i1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S3_L002_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S3_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S3_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:2",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 6,
            "fastq_id": null,
            "fastqs": {
                "i1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S4_L001_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S4_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S4_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "3M-february-2018",
                    },
                ],
                "description": "Single Cell 3' v3",
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "rna": {
                    "length": null,
                    "min_length": 15,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": {
                    "length": 12,
                    "min_length": 10,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 7,
            "fastq_id": null,
            "fastqs": {
                "i1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S4_L002_I1_001.fastq.gz",
                "i2": null,
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S4_L002_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq/PAXUGA_Relapse_S4_L002_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-PAXUGA_Relapse:0:1:HGVV3DRXY:2",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    reference_path              = "/gpfs/data/sequence/cellranger-refdata/refdata-gex-GRCh38-2020-A",
    read_shards                 = {
        corrected_reads: [
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-uac01688b61/files/valid_shard.shard",
            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-uac01688b61/files/valid_shard.shard",
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            "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-uac01688b61/files/valid_shard.shard",
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                offset:    0,
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                whitelist: "3M-february-2018",
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