@include "rna/_basic_sc_rna_counter.mro"

call _BASIC_SC_RNA_COUNTER(
    gem_well                  = 1,
    sample_id                 = "cellranger-Aiptasia-sym_reprep1",
    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,
                },
            ],
        },
    },
    is_antibody_only          = false,
    is_pd                     = false,
    chunks                    = [
        {
            "chemistry": {
                "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,
                    },
                ],
            },
            "chunk_id": 0,
            "fastq_id": null,
            "fastqs": {
                "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_I1_001.fastq.gz",
                "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_I2_001.fastq.gz",
                "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "cellranger-Aiptasia-sym_reprep1:0:1:AAFJ277M5:1",
            "read_lengths": {},
            "subsample_rate": null,
            "umi_extractor": {
                "translators": [null],
            },
        },
    ],
    reference_path            = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-GCA_001417965_1_Aiptasia_genome_1_1_genomic",
    cell_calling_config       = {
        cell_barcodes:                        null,
        disable_ab_aggregate_detection:       false,
        disable_high_occupancy_gem_detection: false,
        emptydrops_minimum_umis: {
            per_gem_well: null,
            per_sample:   null,
        },
        force_cells: {
            per_gem_well: null,
            per_sample:   null,
        },
        global_minimum_umis: {
            per_gem_well: null,
            per_sample:   null,
        },
        max_mito_percent: {
            per_gem_well: null,
            per_sample:   null,
        },
        override_library_types:               null,
        override_mode:                        null,
        recovered_cells: {
            per_gem_well: null,
            per_sample:   null,
        },
    },
    subsample_rate            = null,
    initial_reads             = null,
    r1_length                 = null,
    r2_length                 = null,
    trim_polya_min_score      = 20,
    trim_tso_min_score        = 20,
    min_reads_to_report_bc    = 1000,
    feature_reference         = null,
    target_features           = null,
    target_set                = null,
    target_set_name           = null,
    target_panel_summary      = null,
    include_exons             = true,
    include_introns           = true,
    filter_probes             = null,
    aligner                   = null,
    disable_target_umi_filter = true,
    multi_config_sha          = null,
    no_bam                    = false,
    force_sample_barcodes     = {
        cells_per_tag:        null,
        non_singlet_barcodes: null,
        sample_barcodes:      null,
    },
    disable_multi             = true,
    multi_graph               = null,
    is_spatial                = false,
    is_visium_hd              = false,
    min_assignment_confidence = null,
    slide_serial_capture_area = null,
    feature_config            = null,
    v1_pattern_fix            = null,
)
