# sample_id,molecule_h5
# cellranger-Aiptasia-apo_rep1,/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/outs/molecule_info.h5
# cellranger-Aiptasia-pilot_Apo_Sym,/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-pilot_Apo_Sym/outs/molecule_info.h5
# cellranger-Aiptasia-superloading_Sym,/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-superloading_Sym/outs/molecule_info.h5
# cellranger-Aiptasia-sym_rep1,/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_rep1/outs/molecule_info.h5
# cellranger-Aiptasia-sym_reprep1,/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/outs/molecule_info.h5
# 
@include "rna/sc_rna_aggregator_cs.mro"

call SC_RNA_AGGREGATOR_CS(
    sample_id                = "cellranger-aggr-Aiptasia",
    sample_desc              = "aggr-Aiptasia",
    pipestance_root          = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq",
    aggregation_csv          = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia.csv",
    normalization_mode       = "mapped",
    no_secondary_analysis    = false,
    min_crispr_umi_threshold = 3,
    enable_tsne              = false,
)
