@include "rna/spatial_rna_counter_prep.mro"

call SPATIAL_RNA_COUNTER_PREP(
    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,
        },
    ],
    chemistry_name       = "SPATIAL3Pv1",
    custom_chemistry_def = null,
    reference_path       = "/gpfs/data/yanailab/refs/homo_sapiens/hg38_mm10_10X/hg38_and_mm10",
    r1_length            = null,
    r2_length            = null,
    allowed_chems        = ["SPATIAL3Pv1"],
)
