@include "rna/spatial_rna_counter_cs.mro"

call SPATIAL_RNA_COUNTER_CS(
    sample_id                 = "399-A1",
    sample_def                = [
        {
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/gpfs/data/yanailab/runs/2023-04-15",
            "sample_indices": ["any"],
            "sample_names": ["BS21014A"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    sample_desc               = "",
    slide_serial_capture_area = "V12D12-399-A1",
    loupe_alignment_file      = "/gpfs/home/jw7078/ST-399/V12D12-399-A1.json",
    gpr_file                  = null,
    reference_path            = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    no_bam                    = false,
    no_secondary_analysis     = false,
    rps_limit                 = null,
    r1_length                 = null,
    r2_length                 = null,
    trim_polya_min_score      = 20,
    trim_tso_min_score        = 20,
    tissue_image_paths        = ["/gpfs/home/jw7078/ST-399/ST-399-A1.jpg"],
    dark_images               = 0,
    reorientation_mode        = null,
)
