@include "rna/_cr_aggr_stages.mro"

call MERGE_MOLECULES(
    sample_defs = [
        {
            "library_id": "cellranger-Aiptasia-apo_rep1",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-pilot_Apo_Sym",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-pilot_Apo_Sym/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-superloading_Sym",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-superloading_Sym/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-sym_rep1",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_rep1/outs/molecule_info.h5",
        },
        {
            "library_id": "cellranger-Aiptasia-sym_reprep1",
            "molecule_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/outs/molecule_info.h5",
        },
    ],
    libraries   = [
        {
            "aggr_id": "cellranger-Aiptasia-apo_rep1",
            "batch_id": 0,
            "batch_name": "cellranger-Aiptasia-apo_rep1",
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "old_gem_group": 1,
            "old_library_index": 0,
            "target_set_name": null,
        },
        {
            "aggr_id": "cellranger-Aiptasia-pilot_Apo_Sym",
            "batch_id": 1,
            "batch_name": "cellranger-Aiptasia-pilot_Apo_Sym",
            "gem_group": 2,
            "library_id": 1,
            "library_type": "Gene Expression",
            "old_gem_group": 1,
            "old_library_index": 0,
            "target_set_name": null,
        },
        {
            "aggr_id": "cellranger-Aiptasia-superloading_Sym",
            "batch_id": 2,
            "batch_name": "cellranger-Aiptasia-superloading_Sym",
            "gem_group": 3,
            "library_id": 2,
            "library_type": "Gene Expression",
            "old_gem_group": 1,
            "old_library_index": 0,
            "target_set_name": null,
        },
        {
            "aggr_id": "cellranger-Aiptasia-sym_rep1",
            "batch_id": 3,
            "batch_name": "cellranger-Aiptasia-sym_rep1",
            "gem_group": 4,
            "library_id": 3,
            "library_type": "Gene Expression",
            "old_gem_group": 1,
            "old_library_index": 0,
            "target_set_name": null,
        },
        {
            "aggr_id": "cellranger-Aiptasia-sym_reprep1",
            "batch_id": 4,
            "batch_name": "cellranger-Aiptasia-sym_reprep1",
            "gem_group": 5,
            "library_id": 4,
            "library_type": "Gene Expression",
            "old_gem_group": 1,
            "old_library_index": 0,
            "target_set_name": null,
        },
    ],
)
