@include "rna/_cr_lib_stages.mro"

call MULTI_SETUP_CHUNKS(
    sample_id            = "Nodule_2_gex_only",
    sample_def           = [
        {
            "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,
        },
    ],
    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,
            },
        ],
    },
    default_library_type = null,
)
