@include "_basic_sc_rna_counter.mro"

call _BASIC_SC_RNA_COUNTER(
    sample_id = "h2b_run2",
    chemistry_def = {
        "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
        }
    },
    barcode_whitelist = "3M-february-2018",
    is_antibody_only = false,
    chunks = [
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "read_chunks": {
                "I1": null,
                "I2": null,
                "R1": "/orange/ewang/lancetdenes/190979853/fastq_files/h2b/H2B-myonuclei_S1_L001_R1_001.fastq.gz",
                "R2": "/orange/ewang/lancetdenes/190979853/fastq_files/h2b/H2B-myonuclei_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
        }
    ],
    barcode_confidence_threshold = 0.975,
    umi_min_qual_threshold = 10,
    align = {
        "aligner": "star",
        "high_conf_mapq": null
    },
    align_threads = 4,
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    recovered_cells = 10000,
    force_cells = null,
    cell_barcodes = null,
    correct_barcodes = true,
    rescue_multimappers = true,
    skip_metrics = false,
    skip_translate = {},
    annotation_params = null,
    filter_umis = true,
    retain_fastqs = false,
    subsample_rate = 1,
    initial_reads = null,
    primers = [
        {
            "name": "P5",
            "seq": "AATGATACGGCGACCACCGAGATCT"
        },
        {
            "name": "P7",
            "seq": "CAAGCAGAAGACGGCATACGAGAT"
        },
        {
            "name": "R1",
            "seq": "ACACTCTTTCCCTACACGACG"
        },
        {
            "name": "R2",
            "seq": "GTGACTGGAGTTCAGACGTGTG"
        },
        {
            "name": "switch_oligo",
            "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG"
        },
        {
            "name": "polyA",
            "seq": "AAAAAAAAAAAAAAAAAAAA"
        }
    ],
    r1_length = null,
    r2_length = null,
    feature_reference = null,
    library_info = [
        {
            "gem_group": 1,
            "library_id": "0",
            "library_type": "Gene Expression"
        }
    ],
)