@include "rna/_cr_lib_stages.mro"

call COMBINE_GEM_WELL_CHEMISTRIES(
    gem_well_detect_chemistry = [
        {
            check_barcodes_compatibility: {
                libraries_to_translate: [],
            },
            detect_count_chem: {
                chemistry_def: {
                    barcode: [
                        {
                            "kind": "gel_bead",
                            "length": 16,
                            "offset": 0,
                            "read_type": "R1",
                            "whitelist": {
                                "name": "737K-arc-v1",
                            },
                        },
                    ],
                    description:  "Single Cell Multiome ATAC + Gene Expression v1",
                    endedness:    "three_prime",
                    name:         "ARC-v1",
                    rna: {
                        "length": null,
                        "min_length": null,
                        "offset": 0,
                        "read_type": "R2",
                    },
                    rna2:         null,
                    strandedness: "+",
                    umi: [
                        {
                            "length": 12,
                            "min_length": 10,
                            "offset": 16,
                            "read_type": "R1",
                            "whitelist": null,
                        },
                    ],
                },
                chemistry_type:   "ARC-v1",
                is_antibody_only: false,
            },
            detect_vdj_chem: null,
            sample_defs_count: [
                {
                    "fastq_id": null,
                    "fastq_mode": "ILMN_BCL2FASTQ",
                    "gem_group": null,
                    "lanes": null,
                    "library_type": "Gene Expression",
                    "read_path": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA",
                    "sample_indices": ["any"],
                    "sample_names": ["Nodule_2"],
                    "subsample_rate": null,
                    "target_set": null,
                    "target_set_name": null,
                },
            ],
        },
    ],
)
