@include "rna/spatial_rna_counter_cs.mro"

call SPATIAL_RNA_COUNTER_CS(
    sample_id                 = "ST358_A1",
    sample_def                = [
        {
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A",
            "sample_indices": ["any"],
            "sample_names": ["BS20957A"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    sample_desc               = "",
    slide_serial_capture_area = "V12U06-358-A1",
    loupe_alignment_file      = "/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/V12U06-358-A1_holes.json",
    gpr_file                  = null,
    reference_path            = "/gpfs/data/yanailab/refs/homo_sapiens/hg38_mm10_10X/hg38_and_mm10",
    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/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif"],
    dark_images               = 0,
    reorientation_mode        = null,
)
