@include "rna/_cr_lib_stages.mro"

call ALIGN_AND_COUNT(
    gem_well                    = 1,
    read_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",
    read_shards                 = {
        corrected_reads: [
            "/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/BARCODE_CORRECTION/fork0/chnk00-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk01-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk02-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk03-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk04-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk05-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk06-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk07-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk08-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk09-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk10-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk11-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk12-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk13-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk14-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk15-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk16-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk17-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk18-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk19-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk20-u29f8cf69a6/files/valid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk21-u29f8cf69a6/files/valid_shard.shard",
        ],
        invalid_reads: [
            "/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/BARCODE_CORRECTION/fork0/chnk00-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk01-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk02-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk03-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk04-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk05-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk06-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk07-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk08-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk09-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk10-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk11-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk12-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk13-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk14-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk15-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk16-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk17-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk18-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk19-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk20-u29f8cf69a6/files/invalid_shard.shard",
            "/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/BARCODE_CORRECTION/fork0/chnk21-u29f8cf69a6/files/invalid_shard.shard",
        ],
        valid_reads: ["/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/MAKE_SHARD/fork0/chnk0-u29f8cf6748/files/valid.shard"],
    },
    feature_counts              = "/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/MAKE_SHARD/fork0/join-u29f8cf6748/files/feature_counts.fbc.bincode",
    feature_reference           = "/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/MAKE_SHARD/fork0/split-u29f8cf6748/files/feature_reference.frf.bincode",
    target_set                  = null,
    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,
                },
            ],
        },
    },
    aligner                     = null,
    include_exons               = true,
    include_introns             = true,
    is_pd                       = false,
    no_bam                      = false,
    targeted_umi_min_read_count = null,
    transcriptome_min_score     = 30,
    trim_polya_min_score        = 20,
    trim_tso_min_score          = 20,
    total_barcode_counts        = "/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/BARCODE_CORRECTION/fork0/join-u29f8cf69a6/files/total_barcode_counts.tbcc.bincode",
    barcode_subset              = null,
    chevron_correction_factor   = null,
    chevron_affected_barcodes   = null,
)
