@include "rna/_sc_rna_counter_stages.mro"

call SUMMARIZE_REPORTS(
    chemistry_defs               = {
        "Gene Expression": {
            barcode: [
                {
                    kind:      "gel_bead",
                    length:    16,
                    offset:    0,
                    read_type: "R1",
                    whitelist: {
                        name:                       "3M-february-2018_TRU",
                        part:                       null,
                        slide:                      null,
                        translation:                false,
                        translation_whitelist_path: null,
                    },
                },
            ],
            barcode_extraction: null,
            description:        "Single Cell 3' v3 (polyA)",
            endedness:          "three_prime",
            name:               "SC3Pv3-polyA",
            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,
                },
            ],
        },
    },
    summaries                    = [
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u29f8cfd517/files/summary.json",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u29f8cfd447/files/summary.json",
        null,
        null,
        null,
        null,
    ],
    sample_id                    = "cellranger-Aiptasia-sym_reprep1",
    sample_desc                  = "Aiptasia-sym_reprep1",
    reference_path               = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-GCA_001417965_1_Aiptasia_genome_1_1_genomic",
    analysis                     = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u29f8cfd447/files/analysis",
    barcode_summary_h5           = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u29f8cfca0b/files/barcode_summary.h5",
    filtered_gene_bc_matrices_h5 = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/filtered_matrices_h5.h5",
    filtered_barcodes            = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/filtered_barcodes.csv",
    target_panel_summary         = null,
    antibody_histograms          = null,
    antibody_treemap             = null,
    antigen_histograms           = null,
    antigen_treemap              = null,
    feature_reference            = null,
    target_set_name              = null,
    per_feature_metrics_csv      = null,
    include_introns              = true,
)
