@include "rna/_slfe_cells_reporter.mro"

call _SLFE_CELLS_REPORTER as _CELLS_REPORTER(
    barcode_whitelist       = "3M-february-2018",
    reference_path          = "/gpfs/data/sequence/cellranger-refdata/refdata-gex-GRCh38-2020-A",
    recovered_cells         = null,
    force_cells             = null,
    slfe_feature_reference  = "/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/MAKE_SHARD/fork0/split-uac016887c3/files/feature_reference.frf.bincode",
    target_panel_summary    = null,
    target_set_name         = null,
    matrices_h5             = "/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/WRITE_H5_MATRIX/fork0/chnk0-uac0168a094/files/raw_feature_bc_matrix.h5",
    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,
        },
    ],
    gem_well                = 1,
    report_mol_inputs       = [
        "/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/ALIGN_AND_COUNT/fork0/chnk00-uac01688bfd/files/bc_umi_info.bui",
        "/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/ALIGN_AND_COUNT/fork0/chnk01-uac01688bfd/files/bc_umi_info.bui",
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