@include "sc_rna_counter_cs.mro"

call SC_RNA_COUNTER_CS(
    sample_id = "h2b_run2",
    sample_def = [
        {
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "read_path": "/orange/ewang/lancetdenes/190979853/fastq_files/h2b",
            "sample_indices": [
                "any"
            ],
            "sample_names": [
                "H2B-myonuclei"
            ]
        }
    ],
    sample_desc = "",
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    recovered_cells = 10000,
    no_secondary_analysis = false,
    force_cells = null,
    chemistry = "auto",
    r1_length = null,
    r2_length = null,
    feature_reference = null,
)