@include "rna/_cr_lib_stages.mro"

call WRITE_POS_BAM(
    bam_header                = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u7b8fcf684a/files/bam_header",
    alignments                = [
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u7b8fcf684b/files/pos_sorted.asf",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u7b8fcf684b/files/pos_sorted.asf",
    ],
    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/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz",
                "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz",
                "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "cellranger-Aiptasia-apo_rep1:0:1:GW240319000:5",
            "read_lengths": {},
            "subsample_rate": null,
            "umi_extractor": {
                "translators": [null],
            },
        },
    ],
    target_set_name           = null,
    sample_barcodes           = null,
    slide_serial_capture_area = null,
)
