@include "_basic_sc_rna_counter_stages.mro"

call CHECK_BARCODES_COMPATIBILITY(
    chunks = [
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L001_I1_001.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L001_R1_001.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L001_R2_001.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L001_I1_002.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L001_R1_002.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L001_R2_002.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:2",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L002_I1_001.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L002_R1_001.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L002_R2_001.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:2",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L002_I1_002.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L002_R1_002.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L002_R2_002.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:3",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L003_I1_001.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L003_R1_001.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L003_R2_001.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:3",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L003_I1_002.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L003_R1_002.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L003_R2_002.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:4",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L004_I1_001.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L004_R1_001.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L004_R2_001.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "Nash_3_run:0:1:HH5YNDSXX:4",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L004_I1_002.fastq.gz",
                "I2": null,
                "R1": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L004_R1_002.fastq.gz",
                "R2": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/10X_Nash_3/Sample_NASH-5_0_1_HH5YNDSXX/bamtofastq_S1_L004_R2_002.fastq.gz"
            },
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "reads_interleaved": false
        }
    ],
    barcode_whitelist = "3M-february-2018",
    num_reads_to_check_barcode = null,
    barcode_compatibility_cutoff = null,
)