@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_type:   "SC5P-R2",
                is_antibody_only: false,
            },
            detect_vdj_chem: [
                {
                    chain_type:     "IG",
                    chemistry_type: "SCVDJ-R2",
                    receptor:       "IG",
                },
                {
                    chain_type:     "TR",
                    chemistry_type: "SCVDJ-R2",
                    receptor:       "TR",
                },
            ],
            sample_defs_count: [
                {
                    fastq_id:        "dimitri_RNA",
                    fastq_mode:      "ILMN_BCL2FASTQ",
                    gem_group:       1,
                    lanes:           null,
                    library_type:    "Gene Expression",
                    read_path:       "/scratch/etanis/ST-118/FASTQ/",
                    sample_indices:  null,
                    sample_names:    ["dimitri_RNA"],
                    subsample_rate:  null,
                    target_set:      null,
                    target_set_name: null,
                },
            ],
        },
    ],
)
