@include "sc_rna_counter.mro"

call SC_RNA_COUNTER(
    sample_id = "h2b_run2",
    sample_def = [
        {
            "gem_group": null,
            "lanes": null,
            "sample_names": [
                "H2B-myonuclei"
            ],
            "sample_indices": [
                "any"
            ],
            "fastq_mode": "ILMN_BCL2FASTQ",
            "read_path": "/orange/ewang/lancetdenes/190979853/fastq_files/h2b"
        }
    ],
    chemistry_name = "auto",
    custom_chemistry_def = null,
    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",
    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"
        }
    ],
    recovered_cells = 10000,
    force_cells = null,
    subsample_rate = 1,
    initial_reads = null,
    sample_desc = "",
    r1_length = null,
    r2_length = null,
    annotation_params = null,
    no_secondary_analysis = false,
    filter_umis = true,
    retain_fastqs = false,
    allowed_chems = [
        "auto",
        "custom",
        "threeprime",
        "fiveprime",
        "SC3P_auto",
        "SC5P_auto",
        "SC3Pv1",
        "SC3Pv2",
        "SC3Pv3",
        "SC5P-PE",
        "SC5P-R2",
        "SC5P-R1",
        "SC-FB"
    ],
    library_type_filter = null,
    feature_reference = null,
    num_reads_to_check_barcode = null,
    barcode_compatibility_cutoff = null,
    disable_preflight_local = false,
    cell_barcodes = null,
)