@include "rna/_spatial_preflights.mro"

call SPACERANGER_PREFLIGHT(
    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,
        },
    ],
    chemistry_name            = "SPATIAL3Pv1",
    custom_chemistry_def      = null,
    reference_path            = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    recovered_cells           = null,
    force_cells               = null,
    allowed_chems             = ["SPATIAL3Pv1"],
    r1_length                 = null,
    r2_length                 = null,
    tissue_image_paths        = ["/gpfs/home/jw7078/ST-399/ST-399-A1.jpg"],
    dark_images               = 0,
    loupe_alignment_file      = "/gpfs/home/jw7078/ST-399/V12D12-399-A1.json",
    gpr_file                  = null,
    slide_serial_capture_area = "V12D12-399-A1",
)
