@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: null,
            sample_defs_count: [
                {
                    "fastq_id": null,
                    "fastq_mode": "ILMN_BCL2FASTQ",
                    "gem_group": null,
                    "lanes": null,
                    "library_type": "Gene Expression",
                    "read_path": "/scratch/etanis/ST-118/FASTQ/",
                    "sample_indices": ["any"],
                    "sample_names": ["dimitri_RNA"],
                    "subsample_rate": null,
                    "target_set": null,
                    "target_set_name": null,
                },
                {
                    "fastq_id": null,
                    "fastq_mode": "ILMN_BCL2FASTQ",
                    "gem_group": null,
                    "lanes": null,
                    "library_type": "Gene Expression",
                    "read_path": "/scratch/etanis/ST-118/FASTQ/",
                    "sample_indices": ["any"],
                    "sample_names": ["dimitri_BCR"],
                    "subsample_rate": null,
                    "target_set": null,
                    "target_set_name": null,
                },
                {
                    "fastq_id": null,
                    "fastq_mode": "ILMN_BCL2FASTQ",
                    "gem_group": null,
                    "lanes": null,
                    "library_type": "Gene Expression",
                    "read_path": "/scratch/etanis/ST-118/FASTQ/",
                    "sample_indices": ["any"],
                    "sample_names": ["dimitri_TCR"],
                    "subsample_rate": null,
                    "target_set": null,
                    "target_set_name": null,
                },
            ],
        },
    ],
)
